Gulf of Chiriqui benthic cover
Ana M. Palacio-Castro
2022-08-30
- Setup
- 1. Uva reef
- Explore data
- Data analysis (Aggregated data)
- 2. Stacked categories - Supplement? Uva Island
- 3. Supplementary datasets (Canal del Afuera and Secas)
- Packages used
Setup
1. Uva reef
Import Coral cover data
(Wide format)
# Read data
cover <- read.csv("CoverData/Uva_cover_R1.csv", header=TRUE, sep = ",")
#summary(cover)
# Convert variables and factors to right format
# convert to numeric variables
cover$Pocillopora <- as.numeric(cover$Pocillopora)
cover$Massive <- as.numeric(cover$Other_scleractinians)
cover$Millepora <- as.numeric(cover$Millepora)
cover$Algae<- as.numeric(cover$Algae)
cover$Substrate<- as.numeric(cover$Substrate)
cover$YEAR <- as.numeric(cover$YEAR)
# convert to nominal factors
cover$Location <- as.factor(cover$Location)
# Dates
# Note: all day from a month were converted to the 15th
cover$Date<-as.Date(cover$Date, format = "%Y-%m-%d")
#summary(cover)
str(cover)## 'data.frame': 539 obs. of 112 variables:
## $ YEAR : num 1980 1980 1980 1980 1980 1980 1980 1980 1980 1980 ...
## $ Month : Factor w/ 12 levels "Apr","Aug","Dec",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Location : Factor w/ 3 levels "4x5","Uva_1m2",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Transect : Factor w/ 12 levels "4x5","I","II",..: 2 3 4 5 6 7 8 9 10 11 ...
## $ Date.of.Data.Collection. : Factor w/ 76 levels "01/01/85","01/01/94",..: 75 75 75 75 75 75 75 75 75 75 ...
## $ Date : Date, format: "1980-12-15" "1980-12-15" ...
## $ Depth.m. : int 2 2 2 2 2 2 2 2 2 2 ...
## $ X.of.benth.points : int NA NA NA NA NA NA NA NA NA NA ...
## $ X.of.subst.points : int NA NA NA NA NA NA NA NA NA NA ...
## $ Analysis.by : Factor w/ 9 levels "","?","Peggy Fong",..: 4 4 4 4 4 4 4 4 4 4 ...
## $ Date.of.Analysis : Factor w/ 9 levels "","04/04/17",..: NA NA NA NA NA NA NA NA NA NA ...
## $ Processing : Factor w/ 7 levels "CPCe over Image",..: 6 6 6 6 6 6 6 6 6 6 ...
## $ Transect.Type : Factor w/ 4 levels "Estimated","Permanent",..: 3 3 3 3 3 3 3 3 3 3 ...
## $ Method : Factor w/ 3 levels "Chain_Transect",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ Cycloceris.curvata..CCUR....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Diaseris.distorta..DDIS....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Gardineroseris.planulata..GPLA....coral: num 0 0 0 0 0 0 0 0 0 0 ...
## $ Gpla_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Leptoseris.scabra..LSCA....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.chiriquiensis..PCHI....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.clavus..PCLA....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.gigantea..PGIG....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pgig_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.maldivensis..PMAL....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.varians..PVAR....coral : num 0 0 0 0 0 ...
## $ Pvar_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pvar_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pavona.spp..PAVO....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Porites.lobata..PLOB....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Porites.panamensis..PPAN....coral : num 0.137 0.137 0 0 0 ...
## $ Ppan_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Psammocora.stellata..PSTE....coral : num 0 0 0 0 0 ...
## $ Psammocora.superficialis..PSUP....coral: num 0 0 0 0 0 ...
## $ Psammocora.spp..PSAM....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.capitata..PCAP....coral : num 3.288 0.959 9.178 4.11 0 ...
## $ Pocillopora.damicornis..PDAM....coral : num 3.151 2.603 0.411 2.877 1.781 ...
## $ Pdam_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pdam_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.effusus..PEFF....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.elegans..PELE....coral : num 17.4 0 0 0 0 ...
## $ Pele_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pele_Pale : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.eydouxi..PEYD....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.inflata..PINF....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.ligulata..PLIG....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.meandrina..PMEA....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.verrucosa..PVER....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.woodjonesi..PWOO....coral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Pocillopora.spp..POCI....coral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ RecMort : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Millepora.intricata..MINT....coral : num 0 0 0 3.97 0 ...
## $ Mint_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Millepora.platyphilla..MPLA....coral : num 3.97 0 0 0 0 ...
## $ Mpla_BL : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Astrangia.browni..ABRO....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Astrangia.equatorialis..AEQU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Caryophyllia.sp...CARYSPP....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Cladopsammia.eguchii..CEGU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Cladopsammia.gracilis..CGRA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Culicia.stellata..CSTE....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Oulangia.bradleyi..OBRA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Phyllangia.consagensis..PCON....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Polycyathus.isabela..PISA....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Rhizopsammia.verrilli..RVER....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Rhizopsammia.wellingtoni..RWEL....aherm: int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.coccinea..TCOC....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.faulkneri..TFAU....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.floreana..TFLO....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Tubastraea.tagusensis..TTAG....aherm : int 0 0 0 0 0 0 0 0 0 0 ...
## $ BLCHCoral : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Coral..C. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Gorgonian..GO....go : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Zoanthids..ZO....zo : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Sponge..SPO....spo : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Antipathes.galapagensis..AGAL....bcoral: int 0 0 0 0 0 0 0 0 0 0 ...
## $ Myriopathes.panamensis..MPAN....bcoral : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Balanus..BALA....O : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Algmt : num 0 0 0 0 0 0 0 0 0 0 ...
## $ AlgRub : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa..CAUL....maca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa_Feather.CSER. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Caulerpa_Grape.CRAC. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Coralline.Algae..CALG....calg : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Filamentous.Cyanobacteria..FLCY....maca: num 0 0 0 0 0 0 0 0 0 0 ...
## $ Laurencia : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Macroalgae..MACA....maca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Peysonnelia : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Turf : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Other.Organism..O. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Dead.coral.w..turf.algae..DCA....dca : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Dead.Frame : num 0 0 0 0 0 0 0 0 0 0 ...
## $ DAMFR : num NA NA NA NA NA NA NA NA NA NA ...
## $ Boulder..B. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Sand.Sediment..S. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Rubble..R. : num 72.1 96.3 90.4 89 98.2 ...
## $ Pavement..P. : int 0 0 0 0 0 0 0 0 0 0 ...
## $ Unknown..UNK. : num 0 0 0 0 0 0 0 0 0 0 ...
## $ NA.LOSS : num 0 0 0 0 0 0 0 0 0 0 ...
## $ Tape.edge : num 0 0 0 0 0 0 0 0 0 0 ...
## [list output truncated]Check transects/sample units
Explore data
Pocillopora
- Pre-1982 Pocillopora cover in 4*5 = 77% manually added
- Line = mean
- Boxplots = median
Non-Pocillopora scleractinians (Uva)
- Line = mean
- Boxplots = median
Millepora (Uva)
- Millepora spp. (individual transects)
Data analysis (Aggregated data)
Aggregate data (Pocillopora)
- Hierarchically aggregate by date and location
# Aggregate by Dataset - Month -Year
aggr.location <- aggregate(Pocillopora
~YEAR+Month+Location,
FUN=mean, data=cover)
aggr.location$Year_F<-as.factor(aggr.location$YEAR)
aggr.location$Date<-paste(aggr.location$YEAR, aggr.location$Month, "15", sep = "-")
aggr.location$Date<-as.Date(aggr.location$Date, format = "%Y-%b-%d")
str(aggr.location)## 'data.frame': 88 obs. of 6 variables:
## $ YEAR : num 2016 2017 1984 1985 2014 ...
## $ Month : Factor w/ 12 levels "Apr","Aug","Dec",..: 1 1 2 2 2 2 2 3 3 3 ...
## $ Location : Factor w/ 3 levels "4x5","Uva_1m2",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ Pocillopora: num 57.28 71.659 0.242 0.62 73.07 ...
## $ Year_F : Factor w/ 29 levels "1980","1983",..: 27 28 3 4 25 26 29 1 3 9 ...
## $ Date : Date, format: "2016-04-15" "2017-04-15" ... #write.csv(aggr.location,
# "Outputs/Pocillopora_mean_by_dataset.csv",
# row.names = F)Stats Pocillopora for conceptual model (pooled datasets)
Pocillopora (model 0)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable
Location (Dataset) as a random factor
Model is significant, but ignores high cover pre-1982
Data does not look normally distributed, which is ok, since the coral cover cannot be linear (Year as continuous), unless pre-1982 is removed?
** Do I need to change the intercept options?**
# # All years 1980_2018
# model0 <- lme(
# Pocillopora ~ -1 + YEAR, random = ~1|Location, data=aggr.location)
# summary(model0)
# anova(model0)
#
# plot(ranef(model0)) # Symmetrical scatter effects around zero?
# plot(model0) # plot residuals vs fitted
# resnorm1 <- resid(model0)
# hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
# coef.m1 <- as.data.frame(coef(summary(model0))) # Coefficients of the model
#
# plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
# plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))
#-----
model0 <- lme(
Pocillopora ~ YEAR, random = ~1|Location, data=aggr.location)
summary(model0)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 725.0116 734.829 -358.5058
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 8.911826 14.02862
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3073.5862 277.08378 84 -11.09262 0
## YEAR 1.5485 0.13859 84 11.17316 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.1964839 -0.5889819 -0.2624917 0.4554009 5.4195389
##
## Number of Observations: 88
## Number of Groups: 3 anova(model0) plot(ranef(model0)) # Symmetrical scatter effects around zero?
plot(model0) # plot residuals vs fitted
resnorm1 <- resid(model0)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model0))) # Coefficients of the model
plot(model0, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model0, Pocillopora ~ fitted(.), abline = c(0,1))
Model 0 (data) plot vs (predicted values)
Model_0 <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(colour=Location))+
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
theme(legend.position = c(0.25, 0.8))+
labs(title="Model 1 data")Model 0
- Extract model 1 predicted values
# Create a new data frame for independent variables
NewData_0 <- expand.grid(Location=unique(aggr.location$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.location$YEAR))))
pred_0 <- predict(model0 , newdata=NewData_0, level=0)
#summary(pred_0)
#length(pred_0)- Plot model predictions
# Using model data
Model0_plot <- ggplot(aggr.location,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0 ,0))+
scale_x_continuous("", limits = c(1979, 2018),
breaks = seq(1980, 2018, by=2),
expand = c(0.02,0.02))+
geom_line(data=NewData_0,
aes(y=predict(model0, level=0, newdata=NewData_0)), size=2)+
labs(title="Model 1 prediction")- Compare data and predictions
Model0_All<-grid.arrange(Model_0, Model0_plot, ncol=2)
Pocillopora (model 0b: removing 1980 datapoints)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable (1980 data removed)
- Location (Dataset) as a random factor
aggr.locationb<-filter(aggr.location, YEAR>1983)
summary(aggr.locationb)## YEAR Month Location Pocillopora Year_F
## Min. :1984 Mar :22 4x5 :38 Min. : 0.2145 1985 : 8
## 1st Qu.:1988 Aug :12 Uva_1m2 :18 1st Qu.: 1.5079 1984 : 7
## Median :1997 Jul :10 UvRf-Chains:27 Median :12.9349 1997 : 5
## Mean :1999 Feb : 7 Mean :20.6385 1989 : 3
## 3rd Qu.:2006 Jan : 7 3rd Qu.:33.5717 1990 : 3
## Max. :2018 Apr : 6 Max. :73.5546 1994 : 3
## (Other):19 (Other):54
## Date
## Min. :1984-06-15
## 1st Qu.:1988-10-15
## Median :1997-10-15
## Mean :1999-01-14
## 3rd Qu.:2006-11-13
## Max. :2018-08-15
## - Seems that removing the intercept is an issue…
# All years 1980_2018
model0b <- lme(
Pocillopora ~ YEAR, random = ~1| Location, data=aggr.locationb)
summary(model0b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## AIC BIC logLik
## 630.7988 640.3766 -311.3994
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.05117 9.986885
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3648.888 211.14511 79 -17.28142 0
## YEAR 1.835 0.10554 79 17.38993 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.8626007 -0.5962037 -0.1968177 0.5313649 2.2762352
##
## Number of Observations: 83
## Number of Groups: 3 anova(model0b) print(model0b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## Log-restricted-likelihood: -311.3994
## Fixed: Pocillopora ~ YEAR
## (Intercept) YEAR
## -3648.888298 1.835369
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.05117 9.986885
##
## Number of Observations: 83
## Number of Groups: 3 plot(ranef(model0b)) # Symmetrical scatter effects around zero?
plot(model0b) # plot residuals vs fitted
resnorm1 <- resid(model0b)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model0b))) # Coefficients of the model
plot(model0b, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model0b, Pocillopora ~ fitted(.), abline = c(0,1))
Model 0b (data) plot
Model 0b
- Extract model 1b predicted values
# Create a new data frame for independent variables
NewData_0b <- expand.grid(Location=unique(aggr.locationb$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.locationb$YEAR))))
pred_0b <- predict(model0b, newdata=NewData_0b, level=0)
#summary(pred_0b)
#length(pred_0b)- Plot model predictions
# Using model data
Model0_plotb <- ggplot(aggr.locationb,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0.0,0.0))+
geom_line(data=NewData_0b,
aes(y=predict(model0b, level=0, newdata=NewData_0b)), size=2)+
labs(title="Model 1b prediction")Model 0b (data) plot vs (predicted values)
Model0b_All<-grid.arrange(Model_0b_data, Model0_plotb, ncol=2)
Pocillopora model 1 (+ multiple comparisons among years)
This model includes data from Chiriqui
- Aggregated by location
- Year is a factor
- Location as a random factor
Results:
- Model is significant
- Better normality
model1_final <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Location, data=aggr.location)
summary(model1_final)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 553.5645 617.9682 -245.7823
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.55603 11.48019
##
## Fixed effects: Pocillopora ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F1980 44.29895 10.210061 57 4.338755 0.0001
## Year_F1983 16.57415 9.188955 57 1.803704 0.0766
## Year_F1984 -6.78593 7.632959 57 -0.889030 0.3777
## Year_F1985 -4.34381 7.439948 57 -0.583849 0.5616
## Year_F1986 1.02520 10.210061 57 0.100411 0.9204
## Year_F1987 1.27457 10.210061 57 0.124834 0.9011
## Year_F1988 2.23030 10.210061 57 0.218442 0.8279
## Year_F1989 -2.07795 9.083723 57 -0.228756 0.8199
## Year_F1990 -0.94790 9.083723 57 -0.104352 0.9173
## Year_F1992 4.16000 10.210061 57 0.407441 0.6852
## Year_F1993 4.83406 10.210061 57 0.473461 0.6377
## Year_F1994 3.94642 9.004154 57 0.438289 0.6628
## Year_F1995 10.16016 9.004154 57 1.128386 0.2639
## Year_F1997 13.98328 7.977199 57 1.752906 0.0850
## Year_F1998 15.45352 10.191919 57 1.516252 0.1350
## Year_F2000 19.65706 9.004154 57 2.183110 0.0332
## Year_F2001 20.71683 10.192208 57 2.032614 0.0468
## Year_F2002 29.00607 9.004154 57 3.221409 0.0021
## Year_F2003 31.38803 9.004154 57 3.485950 0.0010
## Year_F2004 36.30428 10.210061 57 3.555736 0.0008
## Year_F2005 34.95335 9.004154 57 3.881914 0.0003
## Year_F2006 43.60831 10.192208 57 4.278593 0.0001
## Year_F2007 38.34011 9.004154 57 4.258047 0.0001
## Year_F2010 43.32774 9.004154 57 4.811973 0.0000
## Year_F2014 46.40007 9.004154 57 5.153185 0.0000
## Year_F2015 47.75547 9.004154 57 5.303715 0.0000
## Year_F2016 40.01622 9.004154 57 4.444195 0.0000
## Year_F2017 54.79270 9.004154 57 6.085269 0.0000
## Year_F2018 56.34970 9.004154 57 6.258189 0.0000
## Correlation:
## Y_F1980 Y_F1983 Y_F1984 Y_F1985 Y_F1986 Y_F1987 Y_F1988 Y_F1989
## Year_F1983 0.409
## Year_F1984 0.492 0.525
## Year_F1985 0.505 0.545 0.689
## Year_F1986 0.368 0.409 0.492 0.505
## Year_F1987 0.368 0.409 0.492 0.505 0.368
## Year_F1988 0.368 0.409 0.492 0.505 0.368 0.368
## Year_F1989 0.413 0.451 0.560 0.573 0.413 0.413 0.413
## Year_F1990 0.413 0.451 0.560 0.573 0.413 0.413 0.413 0.468
## Year_F1992 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F1993 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F1994 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F1995 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F1997 0.453 0.509 0.601 0.618 0.453 0.453 0.453 0.507
## Year_F1998 0.351 0.402 0.460 0.475 0.351 0.351 0.351 0.391
## Year_F2000 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2001 0.351 0.379 0.480 0.489 0.351 0.351 0.351 0.399
## Year_F2002 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2003 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2004 0.368 0.409 0.492 0.505 0.368 0.368 0.368 0.413
## Year_F2005 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2006 0.351 0.379 0.480 0.489 0.351 0.351 0.351 0.399
## Year_F2007 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2010 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2014 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2015 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2016 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2017 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Year_F2018 0.404 0.449 0.540 0.554 0.404 0.404 0.404 0.454
## Y_F1990 Y_F1992 Y_F1993 Y_F1994 Y_F1995 Y_F1997 Y_F1998 Y_F2000
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992 0.413
## Year_F1993 0.413 0.368
## Year_F1994 0.454 0.404 0.404
## Year_F1995 0.454 0.404 0.404 0.458
## Year_F1997 0.507 0.453 0.453 0.517 0.517
## Year_F1998 0.391 0.351 0.351 0.405 0.405 0.461
## Year_F2000 0.454 0.404 0.404 0.458 0.458 0.517 0.405
## Year_F2001 0.399 0.351 0.351 0.405 0.405 0.456 0.355 0.405
## Year_F2002 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2003 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2004 0.413 0.368 0.368 0.404 0.404 0.453 0.351 0.404
## Year_F2005 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2006 0.399 0.351 0.351 0.405 0.405 0.456 0.355 0.405
## Year_F2007 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2010 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2014 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2015 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2016 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2017 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Year_F2018 0.454 0.404 0.404 0.458 0.458 0.517 0.405 0.458
## Y_F2001 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2006 Y_F2007 Y_F2010
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992
## Year_F1993
## Year_F1994
## Year_F1995
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2001
## Year_F2002 0.405
## Year_F2003 0.405 0.458
## Year_F2004 0.351 0.404 0.404
## Year_F2005 0.405 0.458 0.458 0.404
## Year_F2006 0.366 0.405 0.405 0.351 0.405
## Year_F2007 0.405 0.458 0.458 0.404 0.458 0.405
## Year_F2010 0.405 0.458 0.458 0.404 0.458 0.405 0.458
## Year_F2014 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2015 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2016 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2017 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Year_F2018 0.405 0.458 0.458 0.404 0.458 0.405 0.458 0.458
## Y_F2014 Y_F2015 Y_F2016 Y_F2017
## Year_F1983
## Year_F1984
## Year_F1985
## Year_F1986
## Year_F1987
## Year_F1988
## Year_F1989
## Year_F1990
## Year_F1992
## Year_F1993
## Year_F1994
## Year_F1995
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2001
## Year_F2002
## Year_F2003
## Year_F2004
## Year_F2005
## Year_F2006
## Year_F2007
## Year_F2010
## Year_F2014
## Year_F2015 0.458
## Year_F2016 0.458 0.458
## Year_F2017 0.458 0.458 0.458
## Year_F2018 0.458 0.458 0.458 0.458
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.9719022 -0.5347533 -0.1131969 0.6440439 1.9719022
##
## Number of Observations: 88
## Number of Groups: 3 anova(model1_final) plot(ranef(model1_final)) # Symmetrical scatter effects around zero?
plot(model1_final) # plot residuals vs fitted
resnorm1 <- resid(model1_final)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model1_final))) # Coefficients of the model
plot(model1_final, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model1_final, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp emmeans
Year_F.emm<-emmeans(model1_final, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groups write.csv(year_groups, "Outputs/UvaPocilloTukey.csv", row.names = F)Multiple comparisons among years
- Too many lines!
Summary:
- 1980 is different from 1983-2001) -> Coral cover lose after 1981-82 ENSO
- “Recovery” by ~2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
# Multicomp emmeans glht
m.comp_Pocillopora <- glht(model1_final, linfct = mcp(Year_F = "Tukey"))
Model1_multipcomp<-summary(m.comp_Pocillopora, test = univariate())
Model1_multipcomp##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Pocillopora ~ -1 + Year_F, data = aggr.location,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -27.7248 10.5818 -2.620 0.008792 **
## 1984 - 1980 == 0 -51.0849 9.2639 -5.514 3.50e-08 ***
## 1985 - 1980 == 0 -48.6428 9.1054 -5.342 9.18e-08 ***
## 1986 - 1980 == 0 -43.2738 11.4802 -3.769 0.000164 ***
## 1987 - 1980 == 0 -43.0244 11.4802 -3.748 0.000178 ***
## 1988 - 1980 == 0 -42.0687 11.4802 -3.664 0.000248 ***
## 1989 - 1980 == 0 -46.3769 10.4913 -4.421 9.85e-06 ***
## 1990 - 1980 == 0 -45.2469 10.4913 -4.313 1.61e-05 ***
## 1992 - 1980 == 0 -40.1390 11.4802 -3.496 0.000472 ***
## 1993 - 1980 == 0 -39.4649 11.4802 -3.438 0.000587 ***
## 1994 - 1980 == 0 -40.3525 10.5373 -3.830 0.000128 ***
## 1995 - 1980 == 0 -34.1388 10.5373 -3.240 0.001196 **
## 1997 - 1980 == 0 -30.3157 9.6992 -3.126 0.001774 **
## 1998 - 1980 == 0 -28.8454 11.6204 -2.482 0.013053 *
## 2000 - 1980 == 0 -24.6419 10.5373 -2.339 0.019359 *
## 2001 - 1980 == 0 -23.5821 11.6211 -2.029 0.042433 *
## 2002 - 1980 == 0 -15.2929 10.5373 -1.451 0.146692
## 2003 - 1980 == 0 -12.9109 10.5373 -1.225 0.220476
## 2004 - 1980 == 0 -7.9947 11.4802 -0.696 0.486185
## 2005 - 1980 == 0 -9.3456 10.5373 -0.887 0.375127
## 2006 - 1980 == 0 -0.6906 11.6211 -0.059 0.952610
## 2007 - 1980 == 0 -5.9588 10.5373 -0.566 0.571732
## 2010 - 1980 == 0 -0.9712 10.5373 -0.092 0.926564
## 2014 - 1980 == 0 2.1011 10.5373 0.199 0.841950
## 2015 - 1980 == 0 3.4565 10.5373 0.328 0.742891
## 2016 - 1980 == 0 -4.2827 10.5373 -0.406 0.684421
## 2017 - 1980 == 0 10.4938 10.5373 0.996 0.319313
## 2018 - 1980 == 0 12.0507 10.5373 1.144 0.252776
## 1984 - 1983 == 0 -23.3601 8.3105 -2.811 0.004940 **
## 1985 - 1983 == 0 -20.9180 8.0767 -2.590 0.009600 **
## 1986 - 1983 == 0 -15.5490 10.5818 -1.469 0.141723
## 1987 - 1983 == 0 -15.2996 10.5818 -1.446 0.148222
## 1988 - 1983 == 0 -14.3439 10.5818 -1.356 0.175252
## 1989 - 1983 == 0 -18.6521 9.5748 -1.948 0.051411 .
## 1990 - 1983 == 0 -17.5221 9.5748 -1.830 0.067248 .
## 1992 - 1983 == 0 -12.4142 10.5818 -1.173 0.240731
## 1993 - 1983 == 0 -11.7401 10.5818 -1.109 0.267232
## 1994 - 1983 == 0 -12.6277 9.5512 -1.322 0.186131
## 1995 - 1983 == 0 -6.4140 9.5512 -0.672 0.501877
## 1997 - 1983 == 0 -2.5909 8.5680 -0.302 0.762354
## 1998 - 1983 == 0 -1.1206 10.6341 -0.105 0.916073
## 2000 - 1983 == 0 3.0829 9.5512 0.323 0.746864
## 2001 - 1983 == 0 4.1427 10.8348 0.382 0.702204
## 2002 - 1983 == 0 12.4319 9.5512 1.302 0.193050
## 2003 - 1983 == 0 14.8139 9.5512 1.551 0.120902
## 2004 - 1983 == 0 19.7301 10.5818 1.865 0.062247 .
## 2005 - 1983 == 0 18.3792 9.5512 1.924 0.054319 .
## 2006 - 1983 == 0 27.0342 10.8348 2.495 0.012592 *
## 2007 - 1983 == 0 21.7660 9.5512 2.279 0.022675 *
## 2010 - 1983 == 0 26.7536 9.5512 2.801 0.005093 **
## 2014 - 1983 == 0 29.8259 9.5512 3.123 0.001792 **
## 2015 - 1983 == 0 31.1813 9.5512 3.265 0.001096 **
## 2016 - 1983 == 0 23.4421 9.5512 2.454 0.014114 *
## 2017 - 1983 == 0 38.2185 9.5512 4.001 6.30e-05 ***
## 2018 - 1983 == 0 39.7755 9.5512 4.164 3.12e-05 ***
## 1985 - 1984 == 0 2.4421 5.9498 0.410 0.681475
## 1986 - 1984 == 0 7.8111 9.2639 0.843 0.399128
## 1987 - 1984 == 0 8.0605 9.2639 0.870 0.384247
## 1988 - 1984 == 0 9.0162 9.2639 0.973 0.330421
## 1989 - 1984 == 0 4.7080 7.9417 0.593 0.553304
## 1990 - 1984 == 0 5.8380 7.9417 0.735 0.462273
## 1992 - 1984 == 0 10.9459 9.2639 1.182 0.237377
## 1993 - 1984 == 0 11.6200 9.2639 1.254 0.209722
## 1994 - 1984 == 0 10.7324 8.0654 1.331 0.183298
## 1995 - 1984 == 0 16.9461 8.0654 2.101 0.035633 *
## 1997 - 1984 == 0 20.7692 6.9787 2.976 0.002920 **
## 1998 - 1984 == 0 22.2394 9.5173 2.337 0.019452 *
## 2000 - 1984 == 0 26.4430 8.0654 3.279 0.001043 **
## 2001 - 1984 == 0 27.5028 9.3558 2.940 0.003286 **
## 2002 - 1984 == 0 35.7920 8.0654 4.438 9.09e-06 ***
## 2003 - 1984 == 0 38.1740 8.0654 4.733 2.21e-06 ***
## 2004 - 1984 == 0 43.0902 9.2639 4.651 3.30e-06 ***
## 2005 - 1984 == 0 41.7393 8.0654 5.175 2.28e-07 ***
## 2006 - 1984 == 0 50.3942 9.3558 5.386 7.19e-08 ***
## 2007 - 1984 == 0 45.1260 8.0654 5.595 2.21e-08 ***
## 2010 - 1984 == 0 50.1137 8.0654 6.213 5.18e-10 ***
## 2014 - 1984 == 0 53.1860 8.0654 6.594 4.27e-11 ***
## 2015 - 1984 == 0 54.5414 8.0654 6.762 1.36e-11 ***
## 2016 - 1984 == 0 46.8021 8.0654 5.803 6.52e-09 ***
## 2017 - 1984 == 0 61.5786 8.0654 7.635 2.26e-14 ***
## 2018 - 1984 == 0 63.1356 8.0654 7.828 4.88e-15 ***
## 1986 - 1985 == 0 5.3690 9.1054 0.590 0.555424
## 1987 - 1985 == 0 5.6184 9.1054 0.617 0.537209
## 1988 - 1985 == 0 6.5741 9.1054 0.722 0.470293
## 1989 - 1985 == 0 2.2659 7.7760 0.291 0.770751
## 1990 - 1985 == 0 3.3959 7.7760 0.437 0.662316
## 1992 - 1985 == 0 8.5038 9.1054 0.934 0.350339
## 1993 - 1985 == 0 9.1779 9.1054 1.008 0.313473
## 1994 - 1985 == 0 8.2902 7.8830 1.052 0.292954
## 1995 - 1985 == 0 14.5040 7.8830 1.840 0.065781 .
## 1997 - 1985 == 0 18.3271 6.7535 2.714 0.006653 **
## 1998 - 1985 == 0 19.7973 9.3386 2.120 0.034012 *
## 2000 - 1985 == 0 24.0009 7.8830 3.045 0.002330 **
## 2001 - 1985 == 0 25.0606 9.2240 2.717 0.006590 **
## 2002 - 1985 == 0 33.3499 7.8830 4.231 2.33e-05 ***
## 2003 - 1985 == 0 35.7318 7.8830 4.533 5.82e-06 ***
## 2004 - 1985 == 0 40.6481 9.1054 4.464 8.04e-06 ***
## 2005 - 1985 == 0 39.2972 7.8830 4.985 6.19e-07 ***
## 2006 - 1985 == 0 47.9521 9.2240 5.199 2.01e-07 ***
## 2007 - 1985 == 0 42.6839 7.8830 5.415 6.14e-08 ***
## 2010 - 1985 == 0 47.6716 7.8830 6.047 1.47e-09 ***
## 2014 - 1985 == 0 50.7439 7.8830 6.437 1.22e-10 ***
## 2015 - 1985 == 0 52.0993 7.8830 6.609 3.87e-11 ***
## 2016 - 1985 == 0 44.3600 7.8830 5.627 1.83e-08 ***
## 2017 - 1985 == 0 59.1365 7.8830 7.502 6.28e-14 ***
## 2018 - 1985 == 0 60.6935 7.8830 7.699 1.38e-14 ***
## 1987 - 1986 == 0 0.2494 11.4802 0.022 0.982670
## 1988 - 1986 == 0 1.2051 11.4802 0.105 0.916398
## 1989 - 1986 == 0 -3.1032 10.4913 -0.296 0.767395
## 1990 - 1986 == 0 -1.9731 10.4913 -0.188 0.850822
## 1992 - 1986 == 0 3.1348 11.4802 0.273 0.784806
## 1993 - 1986 == 0 3.8089 11.4802 0.332 0.740057
## 1994 - 1986 == 0 2.9212 10.5373 0.277 0.781605
## 1995 - 1986 == 0 9.1350 10.5373 0.867 0.385986
## 1997 - 1986 == 0 12.9581 9.6992 1.336 0.181550
## 1998 - 1986 == 0 14.4283 11.6204 1.242 0.214369
## 2000 - 1986 == 0 18.6319 10.5373 1.768 0.077029 .
## 2001 - 1986 == 0 19.6916 11.6211 1.694 0.090176 .
## 2002 - 1986 == 0 27.9809 10.5373 2.655 0.007921 **
## 2003 - 1986 == 0 30.3628 10.5373 2.881 0.003958 **
## 2004 - 1986 == 0 35.2791 11.4802 3.073 0.002119 **
## 2005 - 1986 == 0 33.9282 10.5373 3.220 0.001283 **
## 2006 - 1986 == 0 42.5831 11.6211 3.664 0.000248 ***
## 2007 - 1986 == 0 37.3149 10.5373 3.541 0.000398 ***
## 2010 - 1986 == 0 42.3025 10.5373 4.015 5.96e-05 ***
## 2014 - 1986 == 0 45.3749 10.5373 4.306 1.66e-05 ***
## 2015 - 1986 == 0 46.7303 10.5373 4.435 9.22e-06 ***
## 2016 - 1986 == 0 38.9910 10.5373 3.700 0.000215 ***
## 2017 - 1986 == 0 53.7675 10.5373 5.103 3.35e-07 ***
## 2018 - 1986 == 0 55.3245 10.5373 5.250 1.52e-07 ***
## 1988 - 1987 == 0 0.9557 11.4802 0.083 0.933652
## 1989 - 1987 == 0 -3.3525 10.4913 -0.320 0.749308
## 1990 - 1987 == 0 -2.2225 10.4913 -0.212 0.832232
## 1992 - 1987 == 0 2.8854 11.4802 0.251 0.801551
## 1993 - 1987 == 0 3.5595 11.4802 0.310 0.756519
## 1994 - 1987 == 0 2.6719 10.5373 0.254 0.799833
## 1995 - 1987 == 0 8.8856 10.5373 0.843 0.399086
## 1997 - 1987 == 0 12.7087 9.6992 1.310 0.190099
## 1998 - 1987 == 0 14.1790 11.6204 1.220 0.222396
## 2000 - 1987 == 0 18.3825 10.5373 1.745 0.081068 .
## 2001 - 1987 == 0 19.4423 11.6211 1.673 0.094325 .
## 2002 - 1987 == 0 27.7315 10.5373 2.632 0.008494 **
## 2003 - 1987 == 0 30.1135 10.5373 2.858 0.004266 **
## 2004 - 1987 == 0 35.0297 11.4802 3.051 0.002278 **
## 2005 - 1987 == 0 33.6788 10.5373 3.196 0.001393 **
## 2006 - 1987 == 0 42.3337 11.6211 3.643 0.000270 ***
## 2007 - 1987 == 0 37.0655 10.5373 3.518 0.000436 ***
## 2010 - 1987 == 0 42.0532 10.5373 3.991 6.58e-05 ***
## 2014 - 1987 == 0 45.1255 10.5373 4.282 1.85e-05 ***
## 2015 - 1987 == 0 46.4809 10.5373 4.411 1.03e-05 ***
## 2016 - 1987 == 0 38.7417 10.5373 3.677 0.000236 ***
## 2017 - 1987 == 0 53.5181 10.5373 5.079 3.80e-07 ***
## 2018 - 1987 == 0 55.0751 10.5373 5.227 1.73e-07 ***
## 1989 - 1988 == 0 -4.3083 10.4913 -0.411 0.681329
## 1990 - 1988 == 0 -3.1782 10.4913 -0.303 0.761937
## 1992 - 1988 == 0 1.9297 11.4802 0.168 0.866513
## 1993 - 1988 == 0 2.6038 11.4802 0.227 0.820576
## 1994 - 1988 == 0 1.7161 10.5373 0.163 0.870627
## 1995 - 1988 == 0 7.9299 10.5373 0.753 0.451718
## 1997 - 1988 == 0 11.7530 9.6992 1.212 0.225608
## 1998 - 1988 == 0 13.2232 11.6204 1.138 0.255148
## 2000 - 1988 == 0 17.4268 10.5373 1.654 0.098163 .
## 2001 - 1988 == 0 18.4865 11.6211 1.591 0.111662
## 2002 - 1988 == 0 26.7758 10.5373 2.541 0.011052 *
## 2003 - 1988 == 0 29.1577 10.5373 2.767 0.005656 **
## 2004 - 1988 == 0 34.0740 11.4802 2.968 0.002997 **
## 2005 - 1988 == 0 32.7230 10.5373 3.105 0.001900 **
## 2006 - 1988 == 0 41.3780 11.6211 3.561 0.000370 ***
## 2007 - 1988 == 0 36.1098 10.5373 3.427 0.000611 ***
## 2010 - 1988 == 0 41.0974 10.5373 3.900 9.61e-05 ***
## 2014 - 1988 == 0 44.1698 10.5373 4.192 2.77e-05 ***
## 2015 - 1988 == 0 45.5252 10.5373 4.320 1.56e-05 ***
## 2016 - 1988 == 0 37.7859 10.5373 3.586 0.000336 ***
## 2017 - 1988 == 0 52.5624 10.5373 4.988 6.09e-07 ***
## 2018 - 1988 == 0 54.1194 10.5373 5.136 2.81e-07 ***
## 1990 - 1989 == 0 1.1301 9.3735 0.121 0.904041
## 1992 - 1989 == 0 6.2380 10.4913 0.595 0.552122
## 1993 - 1989 == 0 6.9120 10.4913 0.659 0.510003
## 1994 - 1989 == 0 6.0244 9.4500 0.638 0.523799
## 1995 - 1989 == 0 12.2381 9.4500 1.295 0.195307
## 1997 - 1989 == 0 16.0612 8.5222 1.885 0.059480 .
## 1998 - 1989 == 0 17.5315 10.6778 1.642 0.100618
## 2000 - 1989 == 0 21.7350 9.4500 2.300 0.021448 *
## 2001 - 1989 == 0 22.7948 10.6114 2.148 0.031703 *
## 2002 - 1989 == 0 31.0840 9.4500 3.289 0.001004 **
## 2003 - 1989 == 0 33.4660 9.4500 3.541 0.000398 ***
## 2004 - 1989 == 0 38.3822 10.4913 3.658 0.000254 ***
## 2005 - 1989 == 0 37.0313 9.4500 3.919 8.90e-05 ***
## 2006 - 1989 == 0 45.6863 10.6114 4.305 1.67e-05 ***
## 2007 - 1989 == 0 40.4181 9.4500 4.277 1.89e-05 ***
## 2010 - 1989 == 0 45.4057 9.4500 4.805 1.55e-06 ***
## 2014 - 1989 == 0 48.4780 9.4500 5.130 2.90e-07 ***
## 2015 - 1989 == 0 49.8334 9.4500 5.273 1.34e-07 ***
## 2016 - 1989 == 0 42.0942 9.4500 4.454 8.41e-06 ***
## 2017 - 1989 == 0 56.8707 9.4500 6.018 1.77e-09 ***
## 2018 - 1989 == 0 58.4277 9.4500 6.183 6.30e-10 ***
## 1992 - 1990 == 0 5.1079 10.4913 0.487 0.626350
## 1993 - 1990 == 0 5.7820 10.4913 0.551 0.581551
## 1994 - 1990 == 0 4.8943 9.4500 0.518 0.604515
## 1995 - 1990 == 0 11.1081 9.4500 1.175 0.239812
## 1997 - 1990 == 0 14.9312 8.5222 1.752 0.079768 .
## 1998 - 1990 == 0 16.4014 10.6778 1.536 0.124530
## 2000 - 1990 == 0 20.6050 9.4500 2.180 0.029226 *
## 2001 - 1990 == 0 21.6647 10.6114 2.042 0.041187 *
## 2002 - 1990 == 0 29.9540 9.4500 3.170 0.001526 **
## 2003 - 1990 == 0 32.3359 9.4500 3.422 0.000622 ***
## 2004 - 1990 == 0 37.2522 10.4913 3.551 0.000384 ***
## 2005 - 1990 == 0 35.9013 9.4500 3.799 0.000145 ***
## 2006 - 1990 == 0 44.5562 10.6114 4.199 2.68e-05 ***
## 2007 - 1990 == 0 39.2880 9.4500 4.157 3.22e-05 ***
## 2010 - 1990 == 0 44.2756 9.4500 4.685 2.80e-06 ***
## 2014 - 1990 == 0 47.3480 9.4500 5.010 5.43e-07 ***
## 2015 - 1990 == 0 48.7034 9.4500 5.154 2.55e-07 ***
## 2016 - 1990 == 0 40.9641 9.4500 4.335 1.46e-05 ***
## 2017 - 1990 == 0 55.7406 9.4500 5.898 3.67e-09 ***
## 2018 - 1990 == 0 57.2976 9.4500 6.063 1.33e-09 ***
## 1993 - 1992 == 0 0.6741 11.4802 0.059 0.953179
## 1994 - 1992 == 0 -0.2136 10.5373 -0.020 0.983829
## 1995 - 1992 == 0 6.0002 10.5373 0.569 0.569069
## 1997 - 1992 == 0 9.8233 9.6992 1.013 0.311158
## 1998 - 1992 == 0 11.2935 11.6204 0.972 0.331114
## 2000 - 1992 == 0 15.4971 10.5373 1.471 0.141374
## 2001 - 1992 == 0 16.5568 11.6211 1.425 0.154239
## 2002 - 1992 == 0 24.8461 10.5373 2.358 0.018377 *
## 2003 - 1992 == 0 27.2280 10.5373 2.584 0.009767 **
## 2004 - 1992 == 0 32.1443 11.4802 2.800 0.005111 **
## 2005 - 1992 == 0 30.7934 10.5373 2.922 0.003474 **
## 2006 - 1992 == 0 39.4483 11.6211 3.395 0.000687 ***
## 2007 - 1992 == 0 34.1801 10.5373 3.244 0.001180 **
## 2010 - 1992 == 0 39.1677 10.5373 3.717 0.000202 ***
## 2014 - 1992 == 0 42.2401 10.5373 4.009 6.11e-05 ***
## 2015 - 1992 == 0 43.5955 10.5373 4.137 3.51e-05 ***
## 2016 - 1992 == 0 35.8562 10.5373 3.403 0.000667 ***
## 2017 - 1992 == 0 50.6327 10.5373 4.805 1.55e-06 ***
## 2018 - 1992 == 0 52.1897 10.5373 4.953 7.31e-07 ***
## 1994 - 1993 == 0 -0.8876 10.5373 -0.084 0.932867
## 1995 - 1993 == 0 5.3261 10.5373 0.505 0.613240
## 1997 - 1993 == 0 9.1492 9.6992 0.943 0.345529
## 1998 - 1993 == 0 10.6195 11.6204 0.914 0.360788
## 2000 - 1993 == 0 14.8230 10.5373 1.407 0.159510
## 2001 - 1993 == 0 15.8828 11.6211 1.367 0.171715
## 2002 - 1993 == 0 24.1720 10.5373 2.294 0.021793 *
## 2003 - 1993 == 0 26.5540 10.5373 2.520 0.011735 *
## 2004 - 1993 == 0 31.4702 11.4802 2.741 0.006120 **
## 2005 - 1993 == 0 30.1193 10.5373 2.858 0.004258 **
## 2006 - 1993 == 0 38.7742 11.6211 3.337 0.000848 ***
## 2007 - 1993 == 0 33.5060 10.5373 3.180 0.001474 **
## 2010 - 1993 == 0 38.4937 10.5373 3.653 0.000259 ***
## 2014 - 1993 == 0 41.5660 10.5373 3.945 7.99e-05 ***
## 2015 - 1993 == 0 42.9214 10.5373 4.073 4.64e-05 ***
## 2016 - 1993 == 0 35.1822 10.5373 3.339 0.000841 ***
## 2017 - 1993 == 0 49.9586 10.5373 4.741 2.13e-06 ***
## 2018 - 1993 == 0 51.5156 10.5373 4.889 1.01e-06 ***
## 1995 - 1994 == 0 6.2137 9.3735 0.663 0.507393
## 1997 - 1994 == 0 10.0369 8.3919 1.196 0.231690
## 1998 - 1994 == 0 11.5071 10.5197 1.094 0.274015
## 2000 - 1994 == 0 15.7106 9.3735 1.676 0.093726 .
## 2001 - 1994 == 0 16.7704 10.5200 1.594 0.110902
## 2002 - 1994 == 0 25.0596 9.3735 2.673 0.007508 **
## 2003 - 1994 == 0 27.4416 9.3735 2.928 0.003416 **
## 2004 - 1994 == 0 32.3579 10.5373 3.071 0.002135 **
## 2005 - 1994 == 0 31.0069 9.3735 3.308 0.000940 ***
## 2006 - 1994 == 0 39.6619 10.5200 3.770 0.000163 ***
## 2007 - 1994 == 0 34.3937 9.3735 3.669 0.000243 ***
## 2010 - 1994 == 0 39.3813 9.3735 4.201 2.65e-05 ***
## 2014 - 1994 == 0 42.4537 9.3735 4.529 5.92e-06 ***
## 2015 - 1994 == 0 43.8090 9.3735 4.674 2.96e-06 ***
## 2016 - 1994 == 0 36.0698 9.3735 3.848 0.000119 ***
## 2017 - 1994 == 0 50.8463 9.3735 5.424 5.81e-08 ***
## 2018 - 1994 == 0 52.4033 9.3735 5.591 2.26e-08 ***
## 1997 - 1995 == 0 3.8231 8.3919 0.456 0.648698
## 1998 - 1995 == 0 5.2934 10.5197 0.503 0.614833
## 2000 - 1995 == 0 9.4969 9.3735 1.013 0.310983
## 2001 - 1995 == 0 10.5567 10.5200 1.003 0.315625
## 2002 - 1995 == 0 18.8459 9.3735 2.011 0.044374 *
## 2003 - 1995 == 0 21.2279 9.3735 2.265 0.023534 *
## 2004 - 1995 == 0 26.1441 10.5373 2.481 0.013097 *
## 2005 - 1995 == 0 24.7932 9.3735 2.645 0.008169 **
## 2006 - 1995 == 0 33.4482 10.5200 3.179 0.001475 **
## 2007 - 1995 == 0 28.1800 9.3735 3.006 0.002644 **
## 2010 - 1995 == 0 33.1676 9.3735 3.538 0.000403 ***
## 2014 - 1995 == 0 36.2399 9.3735 3.866 0.000111 ***
## 2015 - 1995 == 0 37.5953 9.3735 4.011 6.05e-05 ***
## 2016 - 1995 == 0 29.8561 9.3735 3.185 0.001447 **
## 2017 - 1995 == 0 44.6325 9.3735 4.762 1.92e-06 ***
## 2018 - 1995 == 0 46.1895 9.3735 4.928 8.32e-07 ***
## 1998 - 1997 == 0 1.4702 9.6206 0.153 0.878539
## 2000 - 1997 == 0 5.6738 8.3919 0.676 0.498976
## 2001 - 1997 == 0 6.7335 9.6653 0.697 0.486009
## 2002 - 1997 == 0 15.0228 8.3919 1.790 0.073429 .
## 2003 - 1997 == 0 17.4048 8.3919 2.074 0.038080 *
## 2004 - 1997 == 0 22.3210 9.6992 2.301 0.021373 *
## 2005 - 1997 == 0 20.9701 8.3919 2.499 0.012460 *
## 2006 - 1997 == 0 29.6250 9.6653 3.065 0.002176 **
## 2007 - 1997 == 0 24.3568 8.3919 2.902 0.003703 **
## 2010 - 1997 == 0 29.3445 8.3919 3.497 0.000471 ***
## 2014 - 1997 == 0 32.4168 8.3919 3.863 0.000112 ***
## 2015 - 1997 == 0 33.7722 8.3919 4.024 5.71e-05 ***
## 2016 - 1997 == 0 26.0329 8.3919 3.102 0.001921 **
## 2017 - 1997 == 0 40.8094 8.3919 4.863 1.16e-06 ***
## 2018 - 1997 == 0 42.3664 8.3919 5.048 4.45e-07 ***
## 2000 - 1998 == 0 4.2035 10.5197 0.400 0.689460
## 2001 - 1998 == 0 5.2633 11.5733 0.455 0.649266
## 2002 - 1998 == 0 13.5526 10.5197 1.288 0.197640
## 2003 - 1998 == 0 15.9345 10.5197 1.515 0.129840
## 2004 - 1998 == 0 20.8508 11.6204 1.794 0.072761 .
## 2005 - 1998 == 0 19.4998 10.5197 1.854 0.063789 .
## 2006 - 1998 == 0 28.1548 11.5733 2.433 0.014985 *
## 2007 - 1998 == 0 22.8866 10.5197 2.176 0.029585 *
## 2010 - 1998 == 0 27.8742 10.5197 2.650 0.008056 **
## 2014 - 1998 == 0 30.9466 10.5197 2.942 0.003263 **
## 2015 - 1998 == 0 32.3019 10.5197 3.071 0.002136 **
## 2016 - 1998 == 0 24.5627 10.5197 2.335 0.019547 *
## 2017 - 1998 == 0 39.3392 10.5197 3.740 0.000184 ***
## 2018 - 1998 == 0 40.8962 10.5197 3.888 0.000101 ***
## 2001 - 2000 == 0 1.0598 10.5200 0.101 0.919758
## 2002 - 2000 == 0 9.3490 9.3735 0.997 0.318578
## 2003 - 2000 == 0 11.7310 9.3735 1.251 0.210752
## 2004 - 2000 == 0 16.6472 10.5373 1.580 0.114142
## 2005 - 2000 == 0 15.2963 9.3735 1.632 0.102709
## 2006 - 2000 == 0 23.9513 10.5200 2.277 0.022801 *
## 2007 - 2000 == 0 18.6831 9.3735 1.993 0.046243 *
## 2010 - 2000 == 0 23.6707 9.3735 2.525 0.011561 *
## 2014 - 2000 == 0 26.7430 9.3735 2.853 0.004330 **
## 2015 - 2000 == 0 28.0984 9.3735 2.998 0.002721 **
## 2016 - 2000 == 0 20.3592 9.3735 2.172 0.029857 *
## 2017 - 2000 == 0 35.1356 9.3735 3.748 0.000178 ***
## 2018 - 2000 == 0 36.6926 9.3735 3.914 9.06e-05 ***
## 2002 - 2001 == 0 8.2892 10.5200 0.788 0.430724
## 2003 - 2001 == 0 10.6712 10.5200 1.014 0.310403
## 2004 - 2001 == 0 15.5875 11.6211 1.341 0.179822
## 2005 - 2001 == 0 14.2365 10.5200 1.353 0.175964
## 2006 - 2001 == 0 22.8915 11.4802 1.994 0.046152 *
## 2007 - 2001 == 0 17.6233 10.5200 1.675 0.093890 .
## 2010 - 2001 == 0 22.6109 10.5200 2.149 0.031608 *
## 2014 - 2001 == 0 25.6832 10.5200 2.441 0.014631 *
## 2015 - 2001 == 0 27.0386 10.5200 2.570 0.010163 *
## 2016 - 2001 == 0 19.2994 10.5200 1.835 0.066572 .
## 2017 - 2001 == 0 34.0759 10.5200 3.239 0.001199 **
## 2018 - 2001 == 0 35.6329 10.5200 3.387 0.000706 ***
## 2003 - 2002 == 0 2.3820 9.3735 0.254 0.799406
## 2004 - 2002 == 0 7.2982 10.5373 0.693 0.488554
## 2005 - 2002 == 0 5.9473 9.3735 0.634 0.525770
## 2006 - 2002 == 0 14.6022 10.5200 1.388 0.165121
## 2007 - 2002 == 0 9.3340 9.3735 0.996 0.319354
## 2010 - 2002 == 0 14.3217 9.3735 1.528 0.126541
## 2014 - 2002 == 0 17.3940 9.3735 1.856 0.063503 .
## 2015 - 2002 == 0 18.7494 9.3735 2.000 0.045473 *
## 2016 - 2002 == 0 11.0102 9.3735 1.175 0.240155
## 2017 - 2002 == 0 25.7866 9.3735 2.751 0.005941 **
## 2018 - 2002 == 0 27.3436 9.3735 2.917 0.003533 **
## 2004 - 2003 == 0 4.9162 10.5373 0.467 0.640816
## 2005 - 2003 == 0 3.5653 9.3735 0.380 0.703678
## 2006 - 2003 == 0 12.2203 10.5200 1.162 0.245386
## 2007 - 2003 == 0 6.9521 9.3735 0.742 0.458287
## 2010 - 2003 == 0 11.9397 9.3735 1.274 0.202745
## 2014 - 2003 == 0 15.0120 9.3735 1.602 0.109259
## 2015 - 2003 == 0 16.3674 9.3735 1.746 0.080788 .
## 2016 - 2003 == 0 8.6282 9.3735 0.920 0.357320
## 2017 - 2003 == 0 23.4047 9.3735 2.497 0.012529 *
## 2018 - 2003 == 0 24.9617 9.3735 2.663 0.007745 **
## 2005 - 2004 == 0 -1.3509 10.5373 -0.128 0.897987
## 2006 - 2004 == 0 7.3040 11.6211 0.629 0.529668
## 2007 - 2004 == 0 2.0358 10.5373 0.193 0.846800
## 2010 - 2004 == 0 7.0235 10.5373 0.667 0.505068
## 2014 - 2004 == 0 10.0958 10.5373 0.958 0.338010
## 2015 - 2004 == 0 11.4512 10.5373 1.087 0.277155
## 2016 - 2004 == 0 3.7119 10.5373 0.352 0.724637
## 2017 - 2004 == 0 18.4884 10.5373 1.755 0.079332 .
## 2018 - 2004 == 0 20.0454 10.5373 1.902 0.057127 .
## 2006 - 2005 == 0 8.6550 10.5200 0.823 0.410668
## 2007 - 2005 == 0 3.3868 9.3735 0.361 0.717867
## 2010 - 2005 == 0 8.3744 9.3735 0.893 0.371639
## 2014 - 2005 == 0 11.4467 9.3735 1.221 0.222020
## 2015 - 2005 == 0 12.8021 9.3735 1.366 0.172010
## 2016 - 2005 == 0 5.0629 9.3735 0.540 0.589112
## 2017 - 2005 == 0 19.8394 9.3735 2.117 0.034300 *
## 2018 - 2005 == 0 21.3963 9.3735 2.283 0.022452 *
## 2007 - 2006 == 0 -5.2682 10.5200 -0.501 0.616525
## 2010 - 2006 == 0 -0.2806 10.5200 -0.027 0.978723
## 2014 - 2006 == 0 2.7918 10.5200 0.265 0.790718
## 2015 - 2006 == 0 4.1472 10.5200 0.394 0.693420
## 2016 - 2006 == 0 -3.5921 10.5200 -0.341 0.732761
## 2017 - 2006 == 0 11.1844 10.5200 1.063 0.287710
## 2018 - 2006 == 0 12.7414 10.5200 1.211 0.225833
## 2010 - 2007 == 0 4.9876 9.3735 0.532 0.594659
## 2014 - 2007 == 0 8.0600 9.3735 0.860 0.389864
## 2015 - 2007 == 0 9.4154 9.3735 1.004 0.315156
## 2016 - 2007 == 0 1.6761 9.3735 0.179 0.858085
## 2017 - 2007 == 0 16.4526 9.3735 1.755 0.079222 .
## 2018 - 2007 == 0 18.0096 9.3735 1.921 0.054691 .
## 2014 - 2010 == 0 3.0723 9.3735 0.328 0.743088
## 2015 - 2010 == 0 4.4277 9.3735 0.472 0.636667
## 2016 - 2010 == 0 -3.3115 9.3735 -0.353 0.723875
## 2017 - 2010 == 0 11.4650 9.3735 1.223 0.221284
## 2018 - 2010 == 0 13.0220 9.3735 1.389 0.164764
## 2015 - 2014 == 0 1.3554 9.3735 0.145 0.885028
## 2016 - 2014 == 0 -6.3839 9.3735 -0.681 0.495839
## 2017 - 2014 == 0 8.3926 9.3735 0.895 0.370598
## 2018 - 2014 == 0 9.9496 9.3735 1.061 0.288481
## 2016 - 2015 == 0 -7.7392 9.3735 -0.826 0.409003
## 2017 - 2015 == 0 7.0372 9.3735 0.751 0.452799
## 2018 - 2015 == 0 8.5942 9.3735 0.917 0.359215
## 2017 - 2016 == 0 14.7765 9.3735 1.576 0.114933
## 2018 - 2016 == 0 16.3335 9.3735 1.743 0.081419 .
## 2018 - 2017 == 0 1.5570 9.3735 0.166 0.868074
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Figure 1b: Pocillopora coral cover
Model 1 plot (data)
Model1_data <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
stat_summary(fun=mean, geom="line", colour="gray")+
scale_y_continuous("Pocillopora spp. cover (%)", limits = c(-2, 80),
breaks = seq(-0, 80, by=10),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
annotate("rect", xmin = 1983, xmax = 1984,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997.5, xmax = 1998.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015.5, xmax = 2016.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
#ggtitle("Model 2 data")+
theme(legend.position = c(0.25, 0.8))
Model1_data
#ggsave(file="Outputs/Fig_1b.svg", plot=Model2_data, width=7, height=4.3)Figure 1b. b. Pocillopora spp. cover estimated using aggregated data from three datasets. The circles represent the mean values from a dataset for each month-year. The gray line represents the mean Pocillopora cover from all three datasets. The boxplots show the median (second quartile), first and third quartiles, with the bars extending from the minimum to the maximum mean coral cover recorded per dataset. Gray vertical bars demarcate the periods of “very strong” El Niño events (ONI > 2 ºC).
Model 1 (predicted values)
- Extract model 2 predicted values
# Option 1
# Create a new data frame for independent variables
NewData_1 <- expand.grid(Location=unique(aggr.location$Location),
Year_F=unique(aggr.location$Year_F))
pred_1 <- predict(model1_final , newdata=NewData_1, re.form= ~(1|Location),
level=0)
#summary(pred_1)
#length(pred_1)
Predicted_Pocillopora<-cbind(NewData_1, pred_1)
#write.csv(Predicted_Pocillopora, "Model2Predictions.c")
# Option 2
# Effect plot
Model1_plot<-plot(emmeans(model1_final, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 2 predictions") Model1_All<-grid.arrange(Model1_data, Model1_plot, ncol=2)
Aggregate data (Massives)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mas <- aggregate(Massive ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mas$Year_F<-as.factor(aggr.location.mas$YEAR)Massives model (3)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is a continuous variable
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model3 <- lme(
Massive ~ YEAR, random = ~1|Location, data=aggr.location.mas)
summary(Model3)## Linear mixed-effects model fit by REML
## Data: aggr.location.mas
## AIC BIC logLik
## 125.6804 135.451 -58.84018
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 0.6919983 0.4241932
##
## Fixed effects: Massive ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 0.7419698 8.531140 83 0.08697193 0.9309
## YEAR -0.0000404 0.004263 83 -0.00948160 0.9925
## Correlation:
## (Intr)
## YEAR -0.999
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.3877523 -0.5247623 -0.2869986 0.2727082 3.6837232
##
## Number of Observations: 87
## Number of Groups: 3 anova(Model3) #plot(ranef(Model3)) # Symmetrical scatter effects around zero?
#plot(Model3) # plot residuals vs fitted
#resnorm1 <- resid(Model3)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model3))) # Coefficients of the model
#plot(Model3, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model3, Massive ~ fitted(.), abline = c(0,1))Model 3 plot (Massives, non-significant)
Massives model 4 (+ multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
- Model is significant*
# All years 1980_2018
Model4 <- lme(
Massive ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mas)
#summary(Model4)
anova(Model4) plot(ranef(Model4)) # Symmetrical scatter effects around zero?
plot(Model4) # plot residuals vs fitted
resnorm1 <- resid(Model4)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model4))) # Coefficients of the model
plot(Model4, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model4, Massive ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(Model4, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groups write.csv(year_groups, "Outputs/UvaNonPocilloTukey.csv", row.names = F)Multiple comparisons among years
Summary:
- 1980 is different from every year (1983-2018) -> Non-Pocillopora coral cover loss after 1981-82 ENSO has not recovered to pre-1982 values
- 1994-1997 artifact differences by incorporating Uva1m2?
- 1997 marginally different from 1998 (p=0.06)
- 1997 different from 1999-2018 (p<0.05), except 2004-2006 -> Massive coral cover lose after 1997-98 ENSO has not recovered to pre-1997 values
m.comp_Massive <- glht(Model4, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Massive ~ -1 + Year_F, data = aggr.location.mas,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -1.598e+00 4.149e-01 -3.852 0.000117 ***
## 1984 - 1980 == 0 -1.711e+00 3.926e-01 -4.358 1.31e-05 ***
## 1985 - 1980 == 0 -1.712e+00 3.877e-01 -4.415 1.01e-05 ***
## 1986 - 1980 == 0 -1.685e+00 4.426e-01 -3.806 0.000141 ***
## 1987 - 1980 == 0 -1.614e+00 4.426e-01 -3.647 0.000266 ***
## 1988 - 1980 == 0 -1.651e+00 4.426e-01 -3.731 0.000191 ***
## 1989 - 1980 == 0 -1.689e+00 4.197e-01 -4.024 5.71e-05 ***
## 1990 - 1980 == 0 -1.687e+00 4.197e-01 -4.020 5.81e-05 ***
## 1992 - 1980 == 0 -1.563e+00 4.426e-01 -3.531 0.000414 ***
## 1993 - 1980 == 0 -1.374e+00 4.426e-01 -3.104 0.001911 **
## 1994 - 1980 == 0 -1.022e+00 4.191e-01 -2.438 0.014749 *
## 1995 - 1980 == 0 -7.418e-01 4.191e-01 -1.770 0.076716 .
## 1997 - 1980 == 0 -8.880e-01 3.977e-01 -2.233 0.025560 *
## 1998 - 1980 == 0 -1.455e+00 4.439e-01 -3.277 0.001049 **
## 2000 - 1980 == 0 -1.441e+00 4.191e-01 -3.438 0.000585 ***
## 2001 - 1980 == 0 -1.501e+00 4.489e-01 -3.344 0.000826 ***
## 2002 - 1980 == 0 -1.402e+00 4.191e-01 -3.344 0.000825 ***
## 2003 - 1980 == 0 -1.416e+00 4.191e-01 -3.378 0.000731 ***
## 2004 - 1980 == 0 -1.104e+00 4.426e-01 -2.495 0.012604 *
## 2005 - 1980 == 0 -1.394e+00 4.191e-01 -3.326 0.000881 ***
## 2006 - 1980 == 0 -1.257e+00 4.489e-01 -2.800 0.005104 **
## 2007 - 1980 == 0 -1.414e+00 4.191e-01 -3.375 0.000739 ***
## 2010 - 1980 == 0 -1.414e+00 4.191e-01 -3.374 0.000741 ***
## 2014 - 1980 == 0 -1.488e+00 4.191e-01 -3.551 0.000383 ***
## 2015 - 1980 == 0 -1.432e+00 4.191e-01 -3.417 0.000633 ***
## 2016 - 1980 == 0 -1.761e+00 4.191e-01 -4.201 2.66e-05 ***
## 2017 - 1980 == 0 -1.574e+00 4.191e-01 -3.756 0.000172 ***
## 2018 - 1980 == 0 -1.651e+00 4.191e-01 -3.940 8.15e-05 ***
## 1984 - 1983 == 0 -1.129e-01 2.609e-01 -0.433 0.665274
## 1985 - 1983 == 0 -1.134e-01 2.534e-01 -0.448 0.654503
## 1986 - 1983 == 0 -8.662e-02 3.314e-01 -0.261 0.793807
## 1987 - 1983 == 0 -1.597e-02 3.314e-01 -0.048 0.961564
## 1988 - 1983 == 0 -5.316e-02 3.314e-01 -0.160 0.872558
## 1989 - 1983 == 0 -9.082e-02 3.001e-01 -0.303 0.762169
## 1990 - 1983 == 0 -8.914e-02 3.001e-01 -0.297 0.766421
## 1992 - 1983 == 0 3.527e-02 3.314e-01 0.106 0.915237
## 1993 - 1983 == 0 2.244e-01 3.314e-01 0.677 0.498351
## 1994 - 1983 == 0 5.762e-01 2.993e-01 1.925 0.054186 .
## 1995 - 1983 == 0 8.563e-01 2.993e-01 2.861 0.004218 **
## 1997 - 1983 == 0 7.102e-01 2.685e-01 2.645 0.008168 **
## 1998 - 1983 == 0 1.436e-01 3.331e-01 0.431 0.666360
## 2000 - 1983 == 0 1.571e-01 2.993e-01 0.525 0.599608
## 2001 - 1983 == 0 9.711e-02 3.398e-01 0.286 0.775029
## 2002 - 1983 == 0 1.966e-01 2.993e-01 0.657 0.511322
## 2003 - 1983 == 0 1.826e-01 2.993e-01 0.610 0.541859
## 2004 - 1983 == 0 4.939e-01 3.314e-01 1.490 0.136115
## 2005 - 1983 == 0 2.042e-01 2.993e-01 0.682 0.495008
## 2006 - 1983 == 0 3.411e-01 3.398e-01 1.004 0.315486
## 2007 - 1983 == 0 1.839e-01 2.993e-01 0.615 0.538878
## 2010 - 1983 == 0 1.841e-01 2.993e-01 0.615 0.538415
## 2014 - 1983 == 0 1.098e-01 2.993e-01 0.367 0.713591
## 2015 - 1983 == 0 1.661e-01 2.993e-01 0.555 0.578987
## 2016 - 1983 == 0 -1.625e-01 2.993e-01 -0.543 0.587169
## 2017 - 1983 == 0 2.388e-02 2.993e-01 0.080 0.936408
## 2018 - 1983 == 0 -5.308e-02 2.993e-01 -0.177 0.859236
## 1985 - 1984 == 0 -5.331e-04 1.862e-01 -0.003 0.997716
## 1986 - 1984 == 0 2.625e-02 2.901e-01 0.090 0.927907
## 1987 - 1984 == 0 9.690e-02 2.901e-01 0.334 0.738353
## 1988 - 1984 == 0 5.971e-02 2.901e-01 0.206 0.836927
## 1989 - 1984 == 0 2.205e-02 2.486e-01 0.089 0.929329
## 1990 - 1984 == 0 2.372e-02 2.486e-01 0.095 0.923982
## 1992 - 1984 == 0 1.481e-01 2.901e-01 0.511 0.609565
## 1993 - 1984 == 0 3.373e-01 2.901e-01 1.163 0.244967
## 1994 - 1984 == 0 6.891e-01 2.527e-01 2.727 0.006393 **
## 1995 - 1984 == 0 9.692e-01 2.527e-01 3.836 0.000125 ***
## 1997 - 1984 == 0 8.230e-01 2.189e-01 3.760 0.000170 ***
## 1998 - 1984 == 0 2.565e-01 2.984e-01 0.859 0.390111
## 2000 - 1984 == 0 2.700e-01 2.527e-01 1.068 0.285344
## 2001 - 1984 == 0 2.100e-01 2.931e-01 0.716 0.473698
## 2002 - 1984 == 0 3.094e-01 2.527e-01 1.225 0.220761
## 2003 - 1984 == 0 2.954e-01 2.527e-01 1.169 0.242361
## 2004 - 1984 == 0 6.068e-01 2.901e-01 2.092 0.036449 *
## 2005 - 1984 == 0 3.171e-01 2.527e-01 1.255 0.209549
## 2006 - 1984 == 0 4.539e-01 2.931e-01 1.549 0.121413
## 2007 - 1984 == 0 2.968e-01 2.527e-01 1.174 0.240218
## 2010 - 1984 == 0 2.970e-01 2.527e-01 1.175 0.239885
## 2014 - 1984 == 0 2.227e-01 2.527e-01 0.881 0.378128
## 2015 - 1984 == 0 2.789e-01 2.527e-01 1.104 0.269679
## 2016 - 1984 == 0 -4.962e-02 2.527e-01 -0.196 0.844318
## 2017 - 1984 == 0 1.367e-01 2.527e-01 0.541 0.588405
## 2018 - 1984 == 0 5.979e-02 2.527e-01 0.237 0.812954
## 1986 - 1985 == 0 2.678e-02 2.851e-01 0.094 0.925155
## 1987 - 1985 == 0 9.743e-02 2.851e-01 0.342 0.732510
## 1988 - 1985 == 0 6.024e-02 2.851e-01 0.211 0.832637
## 1989 - 1985 == 0 2.258e-02 2.434e-01 0.093 0.926077
## 1990 - 1985 == 0 2.426e-02 2.434e-01 0.100 0.920618
## 1992 - 1985 == 0 1.487e-01 2.851e-01 0.522 0.601977
## 1993 - 1985 == 0 3.378e-01 2.851e-01 1.185 0.236014
## 1994 - 1985 == 0 6.896e-01 2.469e-01 2.793 0.005225 **
## 1995 - 1985 == 0 9.697e-01 2.469e-01 3.927 8.59e-05 ***
## 1997 - 1985 == 0 8.236e-01 2.117e-01 3.890 0.000100 ***
## 1998 - 1985 == 0 2.570e-01 2.927e-01 0.878 0.379978
## 2000 - 1985 == 0 2.705e-01 2.469e-01 1.096 0.273283
## 2001 - 1985 == 0 2.105e-01 2.889e-01 0.729 0.466269
## 2002 - 1985 == 0 3.100e-01 2.469e-01 1.255 0.209370
## 2003 - 1985 == 0 2.960e-01 2.469e-01 1.199 0.230682
## 2004 - 1985 == 0 6.073e-01 2.851e-01 2.131 0.033122 *
## 2005 - 1985 == 0 3.176e-01 2.469e-01 1.286 0.198335
## 2006 - 1985 == 0 4.545e-01 2.889e-01 1.573 0.115751
## 2007 - 1985 == 0 2.973e-01 2.469e-01 1.204 0.228564
## 2010 - 1985 == 0 2.975e-01 2.469e-01 1.205 0.228236
## 2014 - 1985 == 0 2.232e-01 2.469e-01 0.904 0.365931
## 2015 - 1985 == 0 2.795e-01 2.469e-01 1.132 0.257730
## 2016 - 1985 == 0 -4.909e-02 2.469e-01 -0.199 0.842414
## 2017 - 1985 == 0 1.373e-01 2.469e-01 0.556 0.578237
## 2018 - 1985 == 0 6.032e-02 2.469e-01 0.244 0.806991
## 1987 - 1986 == 0 7.065e-02 3.593e-01 0.197 0.844127
## 1988 - 1986 == 0 3.346e-02 3.593e-01 0.093 0.925811
## 1989 - 1986 == 0 -4.196e-03 3.284e-01 -0.013 0.989805
## 1990 - 1986 == 0 -2.523e-03 3.284e-01 -0.008 0.993869
## 1992 - 1986 == 0 1.219e-01 3.593e-01 0.339 0.734436
## 1993 - 1986 == 0 3.110e-01 3.593e-01 0.866 0.386738
## 1994 - 1986 == 0 6.628e-01 3.299e-01 2.009 0.044519 *
## 1995 - 1986 == 0 9.430e-01 3.299e-01 2.858 0.004259 **
## 1997 - 1986 == 0 7.968e-01 3.037e-01 2.623 0.008706 **
## 1998 - 1986 == 0 2.302e-01 3.639e-01 0.633 0.526983
## 2000 - 1986 == 0 2.437e-01 3.299e-01 0.739 0.460031
## 2001 - 1986 == 0 1.837e-01 3.640e-01 0.505 0.613701
## 2002 - 1986 == 0 2.832e-01 3.299e-01 0.858 0.390686
## 2003 - 1986 == 0 2.692e-01 3.299e-01 0.816 0.414534
## 2004 - 1986 == 0 5.806e-01 3.593e-01 1.616 0.106162
## 2005 - 1986 == 0 2.908e-01 3.299e-01 0.882 0.378002
## 2006 - 1986 == 0 4.277e-01 3.640e-01 1.175 0.239977
## 2007 - 1986 == 0 2.705e-01 3.299e-01 0.820 0.412201
## 2010 - 1986 == 0 2.707e-01 3.299e-01 0.821 0.411838
## 2014 - 1986 == 0 1.965e-01 3.299e-01 0.596 0.551490
## 2015 - 1986 == 0 2.527e-01 3.299e-01 0.766 0.443724
## 2016 - 1986 == 0 -7.587e-02 3.299e-01 -0.230 0.818114
## 2017 - 1986 == 0 1.105e-01 3.299e-01 0.335 0.737666
## 2018 - 1986 == 0 3.355e-02 3.299e-01 0.102 0.919007
## 1988 - 1987 == 0 -3.719e-02 3.593e-01 -0.104 0.917565
## 1989 - 1987 == 0 -7.485e-02 3.284e-01 -0.228 0.819713
## 1990 - 1987 == 0 -7.317e-02 3.284e-01 -0.223 0.823676
## 1992 - 1987 == 0 5.124e-02 3.593e-01 0.143 0.886596
## 1993 - 1987 == 0 2.404e-01 3.593e-01 0.669 0.503540
## 1994 - 1987 == 0 5.922e-01 3.299e-01 1.795 0.072651 .
## 1995 - 1987 == 0 8.723e-01 3.299e-01 2.644 0.008189 **
## 1997 - 1987 == 0 7.261e-01 3.037e-01 2.391 0.016813 *
## 1998 - 1987 == 0 1.596e-01 3.639e-01 0.438 0.661030
## 2000 - 1987 == 0 1.731e-01 3.299e-01 0.525 0.599834
## 2001 - 1987 == 0 1.131e-01 3.640e-01 0.311 0.756041
## 2002 - 1987 == 0 2.125e-01 3.299e-01 0.644 0.519434
## 2003 - 1987 == 0 1.985e-01 3.299e-01 0.602 0.547318
## 2004 - 1987 == 0 5.099e-01 3.593e-01 1.419 0.155878
## 2005 - 1987 == 0 2.202e-01 3.299e-01 0.667 0.504499
## 2006 - 1987 == 0 3.570e-01 3.640e-01 0.981 0.326627
## 2007 - 1987 == 0 1.999e-01 3.299e-01 0.606 0.544600
## 2010 - 1987 == 0 2.001e-01 3.299e-01 0.607 0.544177
## 2014 - 1987 == 0 1.258e-01 3.299e-01 0.381 0.702926
## 2015 - 1987 == 0 1.820e-01 3.299e-01 0.552 0.581110
## 2016 - 1987 == 0 -1.465e-01 3.299e-01 -0.444 0.656951
## 2017 - 1987 == 0 3.985e-02 3.299e-01 0.121 0.903858
## 2018 - 1987 == 0 -3.710e-02 3.299e-01 -0.112 0.910450
## 1989 - 1988 == 0 -3.766e-02 3.284e-01 -0.115 0.908711
## 1990 - 1988 == 0 -3.598e-02 3.284e-01 -0.110 0.912750
## 1992 - 1988 == 0 8.844e-02 3.593e-01 0.246 0.805594
## 1993 - 1988 == 0 2.776e-01 3.593e-01 0.772 0.439859
## 1994 - 1988 == 0 6.294e-01 3.299e-01 1.908 0.056424 .
## 1995 - 1988 == 0 9.095e-01 3.299e-01 2.757 0.005835 **
## 1997 - 1988 == 0 7.633e-01 3.037e-01 2.513 0.011963 *
## 1998 - 1988 == 0 1.968e-01 3.639e-01 0.541 0.588727
## 2000 - 1988 == 0 2.103e-01 3.299e-01 0.637 0.523882
## 2001 - 1988 == 0 1.503e-01 3.640e-01 0.413 0.679704
## 2002 - 1988 == 0 2.497e-01 3.299e-01 0.757 0.449079
## 2003 - 1988 == 0 2.357e-01 3.299e-01 0.715 0.474907
## 2004 - 1988 == 0 5.471e-01 3.593e-01 1.523 0.127866
## 2005 - 1988 == 0 2.574e-01 3.299e-01 0.780 0.435296
## 2006 - 1988 == 0 3.942e-01 3.640e-01 1.083 0.278758
## 2007 - 1988 == 0 2.371e-01 3.299e-01 0.719 0.472384
## 2010 - 1988 == 0 2.373e-01 3.299e-01 0.719 0.471992
## 2014 - 1988 == 0 1.630e-01 3.299e-01 0.494 0.621231
## 2015 - 1988 == 0 2.192e-01 3.299e-01 0.664 0.506372
## 2016 - 1988 == 0 -1.093e-01 3.299e-01 -0.331 0.740347
## 2017 - 1988 == 0 7.704e-02 3.299e-01 0.234 0.815356
## 2018 - 1988 == 0 8.651e-05 3.299e-01 0.000 0.999791
## 1990 - 1989 == 0 1.673e-03 2.934e-01 0.006 0.995450
## 1992 - 1989 == 0 1.261e-01 3.284e-01 0.384 0.701010
## 1993 - 1989 == 0 3.152e-01 3.284e-01 0.960 0.337133
## 1994 - 1989 == 0 6.670e-01 2.959e-01 2.254 0.024185 *
## 1995 - 1989 == 0 9.472e-01 2.959e-01 3.201 0.001370 **
## 1997 - 1989 == 0 8.010e-01 2.670e-01 3.000 0.002697 **
## 1998 - 1989 == 0 2.344e-01 3.345e-01 0.701 0.483461
## 2000 - 1989 == 0 2.479e-01 2.959e-01 0.838 0.402111
## 2001 - 1989 == 0 1.879e-01 3.323e-01 0.565 0.571758
## 2002 - 1989 == 0 2.874e-01 2.959e-01 0.971 0.331462
## 2003 - 1989 == 0 2.734e-01 2.959e-01 0.924 0.355557
## 2004 - 1989 == 0 5.848e-01 3.284e-01 1.781 0.074972 .
## 2005 - 1989 == 0 2.950e-01 2.959e-01 0.997 0.318741
## 2006 - 1989 == 0 4.319e-01 3.323e-01 1.299 0.193773
## 2007 - 1989 == 0 2.747e-01 2.959e-01 0.928 0.353189
## 2010 - 1989 == 0 2.749e-01 2.959e-01 0.929 0.352821
## 2014 - 1989 == 0 2.007e-01 2.959e-01 0.678 0.497689
## 2015 - 1989 == 0 2.569e-01 2.959e-01 0.868 0.385341
## 2016 - 1989 == 0 -7.167e-02 2.959e-01 -0.242 0.808616
## 2017 - 1989 == 0 1.147e-01 2.959e-01 0.388 0.698306
## 2018 - 1989 == 0 3.774e-02 2.959e-01 0.128 0.898506
## 1992 - 1990 == 0 1.244e-01 3.284e-01 0.379 0.704789
## 1993 - 1990 == 0 3.135e-01 3.284e-01 0.955 0.339704
## 1994 - 1990 == 0 6.654e-01 2.959e-01 2.249 0.024542 *
## 1995 - 1990 == 0 9.455e-01 2.959e-01 3.195 0.001397 **
## 1997 - 1990 == 0 7.993e-01 2.670e-01 2.994 0.002753 **
## 1998 - 1990 == 0 2.328e-01 3.345e-01 0.696 0.486588
## 2000 - 1990 == 0 2.463e-01 2.959e-01 0.832 0.405294
## 2001 - 1990 == 0 1.863e-01 3.323e-01 0.560 0.575186
## 2002 - 1990 == 0 2.857e-01 2.959e-01 0.966 0.334284
## 2003 - 1990 == 0 2.717e-01 2.959e-01 0.918 0.358509
## 2004 - 1990 == 0 5.831e-01 3.284e-01 1.776 0.075809 .
## 2005 - 1990 == 0 2.934e-01 2.959e-01 0.991 0.321493
## 2006 - 1990 == 0 4.302e-01 3.323e-01 1.294 0.195505
## 2007 - 1990 == 0 2.731e-01 2.959e-01 0.923 0.356128
## 2010 - 1990 == 0 2.733e-01 2.959e-01 0.923 0.355759
## 2014 - 1990 == 0 1.990e-01 2.959e-01 0.672 0.501280
## 2015 - 1990 == 0 2.552e-01 2.959e-01 0.862 0.388444
## 2016 - 1990 == 0 -7.334e-02 2.959e-01 -0.248 0.804239
## 2017 - 1990 == 0 1.130e-01 2.959e-01 0.382 0.702495
## 2018 - 1990 == 0 3.607e-02 2.959e-01 0.122 0.902982
## 1993 - 1992 == 0 1.891e-01 3.593e-01 0.526 0.598668
## 1994 - 1992 == 0 5.409e-01 3.299e-01 1.640 0.101072
## 1995 - 1992 == 0 8.211e-01 3.299e-01 2.489 0.012816 *
## 1997 - 1992 == 0 6.749e-01 3.037e-01 2.222 0.026279 *
## 1998 - 1992 == 0 1.083e-01 3.639e-01 0.298 0.765943
## 2000 - 1992 == 0 1.218e-01 3.299e-01 0.369 0.711899
## 2001 - 1992 == 0 6.183e-02 3.640e-01 0.170 0.865097
## 2002 - 1992 == 0 1.613e-01 3.299e-01 0.489 0.624923
## 2003 - 1992 == 0 1.473e-01 3.299e-01 0.446 0.655271
## 2004 - 1992 == 0 4.587e-01 3.593e-01 1.276 0.201794
## 2005 - 1992 == 0 1.689e-01 3.299e-01 0.512 0.608585
## 2006 - 1992 == 0 3.058e-01 3.640e-01 0.840 0.400832
## 2007 - 1992 == 0 1.486e-01 3.299e-01 0.451 0.652322
## 2010 - 1992 == 0 1.488e-01 3.299e-01 0.451 0.651863
## 2014 - 1992 == 0 7.457e-02 3.299e-01 0.226 0.821170
## 2015 - 1992 == 0 1.308e-01 3.299e-01 0.396 0.691787
## 2016 - 1992 == 0 -1.978e-01 3.299e-01 -0.599 0.548866
## 2017 - 1992 == 0 -1.140e-02 3.299e-01 -0.035 0.972444
## 2018 - 1992 == 0 -8.835e-02 3.299e-01 -0.268 0.788850
## 1994 - 1993 == 0 3.518e-01 3.299e-01 1.066 0.286235
## 1995 - 1993 == 0 6.319e-01 3.299e-01 1.916 0.055420 .
## 1997 - 1993 == 0 4.858e-01 3.037e-01 1.599 0.109733
## 1998 - 1993 == 0 -8.078e-02 3.639e-01 -0.222 0.824342
## 2000 - 1993 == 0 -6.729e-02 3.299e-01 -0.204 0.838387
## 2001 - 1993 == 0 -1.273e-01 3.640e-01 -0.350 0.726547
## 2002 - 1993 == 0 -2.784e-02 3.299e-01 -0.084 0.932756
## 2003 - 1993 == 0 -4.184e-02 3.299e-01 -0.127 0.899089
## 2004 - 1993 == 0 2.695e-01 3.593e-01 0.750 0.453170
## 2005 - 1993 == 0 -2.018e-02 3.299e-01 -0.061 0.951225
## 2006 - 1993 == 0 1.167e-01 3.640e-01 0.321 0.748571
## 2007 - 1993 == 0 -4.049e-02 3.299e-01 -0.123 0.902325
## 2010 - 1993 == 0 -4.028e-02 3.299e-01 -0.122 0.902829
## 2014 - 1993 == 0 -1.145e-01 3.299e-01 -0.347 0.728424
## 2015 - 1993 == 0 -5.834e-02 3.299e-01 -0.177 0.859640
## 2016 - 1993 == 0 -3.869e-01 3.299e-01 -1.173 0.240907
## 2017 - 1993 == 0 -2.005e-01 3.299e-01 -0.608 0.543316
## 2018 - 1993 == 0 -2.775e-01 3.299e-01 -0.841 0.400310
## 1995 - 1994 == 0 2.801e-01 2.934e-01 0.955 0.339666
## 1997 - 1994 == 0 1.340e-01 2.627e-01 0.510 0.610048
## 1998 - 1994 == 0 -4.326e-01 3.293e-01 -1.314 0.189004
## 2000 - 1994 == 0 -4.191e-01 2.934e-01 -1.428 0.153157
## 2001 - 1994 == 0 -4.791e-01 3.293e-01 -1.455 0.145753
## 2002 - 1994 == 0 -3.796e-01 2.934e-01 -1.294 0.195662
## 2003 - 1994 == 0 -3.936e-01 2.934e-01 -1.342 0.179685
## 2004 - 1994 == 0 -8.227e-02 3.299e-01 -0.249 0.803077
## 2005 - 1994 == 0 -3.720e-01 2.934e-01 -1.268 0.204829
## 2006 - 1994 == 0 -2.352e-01 3.293e-01 -0.714 0.475227
## 2007 - 1994 == 0 -3.923e-01 2.934e-01 -1.337 0.181181
## 2010 - 1994 == 0 -3.921e-01 2.934e-01 -1.336 0.181415
## 2014 - 1994 == 0 -4.664e-01 2.934e-01 -1.590 0.111933
## 2015 - 1994 == 0 -4.102e-01 2.934e-01 -1.398 0.162122
## 2016 - 1994 == 0 -7.387e-01 2.934e-01 -2.518 0.011809 *
## 2017 - 1994 == 0 -5.523e-01 2.934e-01 -1.883 0.059758 .
## 2018 - 1994 == 0 -6.293e-01 2.934e-01 -2.145 0.031963 *
## 1997 - 1995 == 0 -1.462e-01 2.627e-01 -0.556 0.577902
## 1998 - 1995 == 0 -7.127e-01 3.293e-01 -2.164 0.030454 *
## 2000 - 1995 == 0 -6.992e-01 2.934e-01 -2.383 0.017158 *
## 2001 - 1995 == 0 -7.592e-01 3.293e-01 -2.305 0.021151 *
## 2002 - 1995 == 0 -6.598e-01 2.934e-01 -2.249 0.024523 *
## 2003 - 1995 == 0 -6.738e-01 2.934e-01 -2.297 0.021644 *
## 2004 - 1995 == 0 -3.624e-01 3.299e-01 -1.099 0.271978
## 2005 - 1995 == 0 -6.521e-01 2.934e-01 -2.223 0.026233 *
## 2006 - 1995 == 0 -5.153e-01 3.293e-01 -1.565 0.117681
## 2007 - 1995 == 0 -6.724e-01 2.934e-01 -2.292 0.021908 *
## 2010 - 1995 == 0 -6.722e-01 2.934e-01 -2.291 0.021950 *
## 2014 - 1995 == 0 -7.465e-01 2.934e-01 -2.544 0.010947 *
## 2015 - 1995 == 0 -6.903e-01 2.934e-01 -2.353 0.018633 *
## 2016 - 1995 == 0 -1.019e+00 2.934e-01 -3.473 0.000515 ***
## 2017 - 1995 == 0 -8.325e-01 2.934e-01 -2.837 0.004548 **
## 2018 - 1995 == 0 -9.094e-01 2.934e-01 -3.100 0.001937 **
## 1998 - 1997 == 0 -5.666e-01 3.012e-01 -1.881 0.059930 .
## 2000 - 1997 == 0 -5.531e-01 2.627e-01 -2.105 0.035250 *
## 2001 - 1997 == 0 -6.131e-01 3.026e-01 -2.026 0.042793 *
## 2002 - 1997 == 0 -5.136e-01 2.627e-01 -1.955 0.050548 .
## 2003 - 1997 == 0 -5.276e-01 2.627e-01 -2.009 0.044580 *
## 2004 - 1997 == 0 -2.162e-01 3.037e-01 -0.712 0.476505
## 2005 - 1997 == 0 -5.060e-01 2.627e-01 -1.926 0.054086 .
## 2006 - 1997 == 0 -3.691e-01 3.026e-01 -1.220 0.222592
## 2007 - 1997 == 0 -5.263e-01 2.627e-01 -2.003 0.045128 *
## 2010 - 1997 == 0 -5.261e-01 2.627e-01 -2.003 0.045214 *
## 2014 - 1997 == 0 -6.003e-01 2.627e-01 -2.285 0.022289 *
## 2015 - 1997 == 0 -5.441e-01 2.627e-01 -2.071 0.038320 *
## 2016 - 1997 == 0 -8.727e-01 2.627e-01 -3.322 0.000893 ***
## 2017 - 1997 == 0 -6.863e-01 2.627e-01 -2.613 0.008984 **
## 2018 - 1997 == 0 -7.633e-01 2.627e-01 -2.906 0.003665 **
## 2000 - 1998 == 0 1.350e-02 3.293e-01 0.041 0.967314
## 2001 - 1998 == 0 -4.651e-02 3.624e-01 -0.128 0.897898
## 2002 - 1998 == 0 5.294e-02 3.293e-01 0.161 0.872281
## 2003 - 1998 == 0 3.895e-02 3.293e-01 0.118 0.905866
## 2004 - 1998 == 0 3.503e-01 3.639e-01 0.963 0.335748
## 2005 - 1998 == 0 6.060e-02 3.293e-01 0.184 0.854005
## 2006 - 1998 == 0 1.974e-01 3.624e-01 0.545 0.585909
## 2007 - 1998 == 0 4.029e-02 3.293e-01 0.122 0.902623
## 2010 - 1998 == 0 4.050e-02 3.293e-01 0.123 0.902117
## 2014 - 1998 == 0 -3.377e-02 3.293e-01 -0.103 0.918333
## 2015 - 1998 == 0 2.244e-02 3.293e-01 0.068 0.945668
## 2016 - 1998 == 0 -3.061e-01 3.293e-01 -0.929 0.352655
## 2017 - 1998 == 0 -1.197e-01 3.293e-01 -0.364 0.716183
## 2018 - 1998 == 0 -1.967e-01 3.293e-01 -0.597 0.550356
## 2001 - 2000 == 0 -6.000e-02 3.293e-01 -0.182 0.855439
## 2002 - 2000 == 0 3.945e-02 2.934e-01 0.134 0.893039
## 2003 - 2000 == 0 2.545e-02 2.934e-01 0.087 0.930874
## 2004 - 2000 == 0 3.368e-01 3.299e-01 1.021 0.307251
## 2005 - 2000 == 0 4.711e-02 2.934e-01 0.161 0.872442
## 2006 - 2000 == 0 1.839e-01 3.293e-01 0.559 0.576492
## 2007 - 2000 == 0 2.680e-02 2.934e-01 0.091 0.927222
## 2010 - 2000 == 0 2.701e-02 2.934e-01 0.092 0.926653
## 2014 - 2000 == 0 -4.726e-02 2.934e-01 -0.161 0.872018
## 2015 - 2000 == 0 8.948e-03 2.934e-01 0.030 0.975669
## 2016 - 2000 == 0 -3.196e-01 2.934e-01 -1.089 0.276009
## 2017 - 2000 == 0 -1.332e-01 2.934e-01 -0.454 0.649751
## 2018 - 2000 == 0 -2.102e-01 2.934e-01 -0.716 0.473746
## 2002 - 2001 == 0 9.945e-02 3.293e-01 0.302 0.762680
## 2003 - 2001 == 0 8.545e-02 3.293e-01 0.259 0.795283
## 2004 - 2001 == 0 3.968e-01 3.640e-01 1.090 0.275579
## 2005 - 2001 == 0 1.071e-01 3.293e-01 0.325 0.745021
## 2006 - 2001 == 0 2.439e-01 3.593e-01 0.679 0.497203
## 2007 - 2001 == 0 8.680e-02 3.293e-01 0.264 0.792126
## 2010 - 2001 == 0 8.701e-02 3.293e-01 0.264 0.791634
## 2014 - 2001 == 0 1.274e-02 3.293e-01 0.039 0.969150
## 2015 - 2001 == 0 6.895e-02 3.293e-01 0.209 0.834173
## 2016 - 2001 == 0 -2.596e-01 3.293e-01 -0.788 0.430569
## 2017 - 2001 == 0 -7.323e-02 3.293e-01 -0.222 0.824043
## 2018 - 2001 == 0 -1.502e-01 3.293e-01 -0.456 0.648388
## 2003 - 2002 == 0 -1.400e-02 2.934e-01 -0.048 0.961943
## 2004 - 2002 == 0 2.974e-01 3.299e-01 0.901 0.367360
## 2005 - 2002 == 0 7.657e-03 2.934e-01 0.026 0.979180
## 2006 - 2002 == 0 1.445e-01 3.293e-01 0.439 0.660853
## 2007 - 2002 == 0 -1.265e-02 2.934e-01 -0.043 0.965607
## 2010 - 2002 == 0 -1.244e-02 2.934e-01 -0.042 0.966177
## 2014 - 2002 == 0 -8.671e-02 2.934e-01 -0.296 0.767570
## 2015 - 2002 == 0 -3.050e-02 2.934e-01 -0.104 0.917201
## 2016 - 2002 == 0 -3.590e-01 2.934e-01 -1.224 0.221032
## 2017 - 2002 == 0 -1.727e-01 2.934e-01 -0.589 0.556151
## 2018 - 2002 == 0 -2.496e-01 2.934e-01 -0.851 0.394848
## 2004 - 2003 == 0 3.114e-01 3.299e-01 0.944 0.345240
## 2005 - 2003 == 0 2.166e-02 2.934e-01 0.074 0.941160
## 2006 - 2003 == 0 1.585e-01 3.293e-01 0.481 0.630344
## 2007 - 2003 == 0 1.348e-03 2.934e-01 0.005 0.996333
## 2010 - 2003 == 0 1.558e-03 2.934e-01 0.005 0.995762
## 2014 - 2003 == 0 -7.271e-02 2.934e-01 -0.248 0.804258
## 2015 - 2003 == 0 -1.650e-02 2.934e-01 -0.056 0.955146
## 2016 - 2003 == 0 -3.450e-01 2.934e-01 -1.176 0.239566
## 2017 - 2003 == 0 -1.587e-01 2.934e-01 -0.541 0.588609
## 2018 - 2003 == 0 -2.356e-01 2.934e-01 -0.803 0.421892
## 2005 - 2004 == 0 -2.897e-01 3.299e-01 -0.878 0.379824
## 2006 - 2004 == 0 -1.529e-01 3.640e-01 -0.420 0.674443
## 2007 - 2004 == 0 -3.100e-01 3.299e-01 -0.940 0.347333
## 2010 - 2004 == 0 -3.098e-01 3.299e-01 -0.939 0.347659
## 2014 - 2004 == 0 -3.841e-01 3.299e-01 -1.164 0.244313
## 2015 - 2004 == 0 -3.279e-01 3.299e-01 -0.994 0.320280
## 2016 - 2004 == 0 -6.564e-01 3.299e-01 -1.990 0.046616 *
## 2017 - 2004 == 0 -4.701e-01 3.299e-01 -1.425 0.154198
## 2018 - 2004 == 0 -5.470e-01 3.299e-01 -1.658 0.097294 .
## 2006 - 2005 == 0 1.368e-01 3.293e-01 0.415 0.677785
## 2007 - 2005 == 0 -2.031e-02 2.934e-01 -0.069 0.944817
## 2010 - 2005 == 0 -2.010e-02 2.934e-01 -0.069 0.945387
## 2014 - 2005 == 0 -9.437e-02 2.934e-01 -0.322 0.747716
## 2015 - 2005 == 0 -3.816e-02 2.934e-01 -0.130 0.896520
## 2016 - 2005 == 0 -3.667e-01 2.934e-01 -1.250 0.211342
## 2017 - 2005 == 0 -1.803e-01 2.934e-01 -0.615 0.538775
## 2018 - 2005 == 0 -2.573e-01 2.934e-01 -0.877 0.380511
## 2007 - 2006 == 0 -1.571e-01 3.293e-01 -0.477 0.633257
## 2010 - 2006 == 0 -1.569e-01 3.293e-01 -0.477 0.633711
## 2014 - 2006 == 0 -2.312e-01 3.293e-01 -0.702 0.482664
## 2015 - 2006 == 0 -1.750e-01 3.293e-01 -0.531 0.595178
## 2016 - 2006 == 0 -5.035e-01 3.293e-01 -1.529 0.126285
## 2017 - 2006 == 0 -3.172e-01 3.293e-01 -0.963 0.335524
## 2018 - 2006 == 0 -3.941e-01 3.293e-01 -1.197 0.231423
## 2010 - 2007 == 0 2.101e-04 2.934e-01 0.001 0.999429
## 2014 - 2007 == 0 -7.406e-02 2.934e-01 -0.252 0.800704
## 2015 - 2007 == 0 -1.785e-02 2.934e-01 -0.061 0.951485
## 2016 - 2007 == 0 -3.464e-01 2.934e-01 -1.181 0.237734
## 2017 - 2007 == 0 -1.600e-01 2.934e-01 -0.545 0.585445
## 2018 - 2007 == 0 -2.370e-01 2.934e-01 -0.808 0.419241
## 2014 - 2010 == 0 -7.427e-02 2.934e-01 -0.253 0.800151
## 2015 - 2010 == 0 -1.806e-02 2.934e-01 -0.062 0.950915
## 2016 - 2010 == 0 -3.466e-01 2.934e-01 -1.181 0.237450
## 2017 - 2010 == 0 -1.602e-01 2.934e-01 -0.546 0.584952
## 2018 - 2010 == 0 -2.372e-01 2.934e-01 -0.808 0.418829
## 2015 - 2014 == 0 5.621e-02 2.934e-01 0.192 0.848060
## 2016 - 2014 == 0 -2.723e-01 2.934e-01 -0.928 0.353287
## 2017 - 2014 == 0 -8.597e-02 2.934e-01 -0.293 0.769512
## 2018 - 2014 == 0 -1.629e-01 2.934e-01 -0.555 0.578688
## 2016 - 2015 == 0 -3.285e-01 2.934e-01 -1.120 0.262788
## 2017 - 2015 == 0 -1.422e-01 2.934e-01 -0.485 0.627955
## 2018 - 2015 == 0 -2.191e-01 2.934e-01 -0.747 0.455126
## 2017 - 2016 == 0 1.864e-01 2.934e-01 0.635 0.525286
## 2018 - 2016 == 0 1.094e-01 2.934e-01 0.373 0.709201
## 2018 - 2017 == 0 -7.695e-02 2.934e-01 -0.262 0.793098
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 4 plot (Massives, significant)
Model4_All<-grid.arrange(massives_plot, model4_plot, ncol=2)
Aggregate data (Millepora)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mill <- aggregate(Millepora ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mill$Year_F<-as.factor(aggr.location.mill$YEAR)Millepora model (5)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is continuous
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model5 <- lme(Millepora ~ YEAR, random = ~1|Location, data=aggr.location.mill)
summary(Model5)## Linear mixed-effects model fit by REML
## Data: aggr.location.mill
## AIC BIC logLik
## 377.6839 387.4545 -184.8419
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 1.036569 1.914402
##
## Fixed effects: Millepora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 57.58958 38.17441 83 1.508591 0.1352
## YEAR -0.02853 0.01909 83 -1.494158 0.1389
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -0.88787712 -0.19988893 -0.11320291 0.09071803 6.59088878
##
## Number of Observations: 87
## Number of Groups: 3 anova(Model5) #plot(ranef(Model5)) # Symmetrical scatter effects around zero?
#plot(Model5) # plot residuals vs fitted
#resnorm1 <- resid(Model5)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model5))) # Coefficients of the model
#plot(Model5, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model5, Millepora ~ fitted(.), abline = c(0,1))Millepora model 6 (multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
# All years 1980_2018
Model6 <- lme(
Millepora ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mill)
#summary(Model6)
anova(Model6)Millepora plots (non-significant models)
Aggregate data (all Scleractinians)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.scl <- aggregate(All_Corals ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.scl$Year_F<-as.factor(aggr.location.scl$YEAR)All scleractinians (model 7)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR as a continuous variable
- Location as a random factor
Model is significant
# All years 1980_2018
Model7 <- lme(All_Corals ~ YEAR, random = ~1|Location, data=aggr.location.scl)
summary(Model7)## Linear mixed-effects model fit by REML
## Data: aggr.location.scl
## AIC BIC logLik
## 727.2946 737.112 -359.6473
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 9.033042 14.216
##
## Fixed effects: All_Corals ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3018.5300 280.78547 84 -10.75031 0
## YEAR 1.5216 0.14045 84 10.83406 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.1579451 -0.6162544 -0.2954427 0.4970609 5.2973659
##
## Number of Observations: 88
## Number of Groups: 3 anova(Model7) plot(ranef(Model7)) # Symmetrical scatter effects around zero?
plot(Model7) # plot residuals vs fitted
resnorm1 <- resid(Model7)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model7))) # Coefficients of the model
plot(Model7, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model7, All_Corals ~ fitted(.), abline = c(0,1))
Model 7 plot
Scleractinian_plot <- ggplot(aggr.location.scl,
aes(x=YEAR, y=All_Corals)) +
#geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
#stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Coral cover (%)", limits = c(-0.5, 80), expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1979, 2019, by=2), expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")
Scleractinian_plot + theme(legend.position = c(0.25, 0.8))
Scleractinians model 8 (multiple comparisons between years)
This model includes data from Chiriqui
- Aggregated by location
- Year as a factor
- Location as a random factor
# All years 1980_2018
Model8 <- lme(
All_Corals ~ -1 + Year_F, random = ~1|Location, data=aggr.location.scl)
#summary(Model8)
anova(Model8) plot(ranef(Model8)) # Symmetrical scatter effects around zero?
plot(Model8) # plot residuals vs fitted
resnorm1 <- resid(Model8)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model8))) # Coefficients of the model
plot(Model8, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model8, All_Corals ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm_scle<-emmeans(Model8, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups_Scle<-cld(Year_F.emm_scle, by=NULL) # compact-letter display
year_groups_Scle
Model 8 plot data
Model 8 plot
# Effect plot
Model8_predictoin<-plot(emmeans(Model8, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()+
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 8 predictions (All scleractinians)") Model8_All<-grid.arrange(Scleractinian_plot, Model8_predictoin, ncol=2)
Summary:
Pretty much the same as only Pocillopora …
- 1980 is different from 1983-2001 -> Coral cover lose after 1981-82 ENSO
- “Recovery” by 2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
- 1997 not different from 1998, 2000, 2001, 2003
2015 not different from 2016, 2017, 2018
m.comp_sclera <- glht(Model8, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_sclera, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = All_Corals ~ -1 + Year_F, data = aggr.location.scl,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -28.6380 10.8980 -2.628 0.008593 **
## 1984 - 1980 == 0 -52.3502 9.5407 -5.487 4.09e-08 ***
## 1985 - 1980 == 0 -49.9089 9.3775 -5.322 1.03e-07 ***
## 1986 - 1980 == 0 -44.5140 11.8233 -3.765 0.000167 ***
## 1987 - 1980 == 0 -44.1940 11.8233 -3.738 0.000186 ***
## 1988 - 1980 == 0 -43.2755 11.8233 -3.660 0.000252 ***
## 1989 - 1980 == 0 -47.6223 10.8048 -4.408 1.05e-05 ***
## 1990 - 1980 == 0 -46.4883 10.8048 -4.303 1.69e-05 ***
## 1992 - 1980 == 0 -41.2590 11.8233 -3.490 0.000484 ***
## 1993 - 1980 == 0 -40.3945 11.8233 -3.417 0.000634 ***
## 1994 - 1980 == 0 -39.9292 10.8521 -3.679 0.000234 ***
## 1995 - 1980 == 0 -31.0275 10.8521 -2.859 0.004248 **
## 1997 - 1980 == 0 -28.4906 9.9890 -2.852 0.004342 **
## 1998 - 1980 == 0 -30.6310 11.9675 -2.560 0.010482 *
## 2000 - 1980 == 0 -26.1579 10.8521 -2.410 0.015935 *
## 2001 - 1980 == 0 -25.4153 11.9683 -2.124 0.033708 *
## 2002 - 1980 == 0 -16.7682 10.8521 -1.545 0.122309
## 2003 - 1980 == 0 -14.4000 10.8521 -1.327 0.184532
## 2004 - 1980 == 0 -8.6560 11.8233 -0.732 0.464099
## 2005 - 1980 == 0 -10.8151 10.8521 -0.997 0.318965
## 2006 - 1980 == 0 -2.2793 11.9683 -0.190 0.848958
## 2007 - 1980 == 0 -7.4482 10.8521 -0.686 0.492499
## 2010 - 1980 == 0 -2.4605 10.8521 -0.227 0.820636
## 2014 - 1980 == 0 0.5400 10.8521 0.050 0.960310
## 2015 - 1980 == 0 1.9508 10.8521 0.180 0.857339
## 2016 - 1980 == 0 -6.1193 10.8521 -0.564 0.572835
## 2017 - 1980 == 0 8.8441 10.8521 0.815 0.415091
## 2018 - 1980 == 0 10.3253 10.8521 0.951 0.341372
## 1984 - 1983 == 0 -23.7122 8.5587 -2.771 0.005596 **
## 1985 - 1983 == 0 -21.2709 8.3179 -2.557 0.010551 *
## 1986 - 1983 == 0 -15.8760 10.8980 -1.457 0.145176
## 1987 - 1983 == 0 -15.5560 10.8980 -1.427 0.153459
## 1988 - 1983 == 0 -14.6375 10.8980 -1.343 0.179227
## 1989 - 1983 == 0 -18.9844 9.8609 -1.925 0.054202 .
## 1990 - 1983 == 0 -17.8504 9.8609 -1.810 0.070261 .
## 1992 - 1983 == 0 -12.6210 10.8980 -1.158 0.246821
## 1993 - 1983 == 0 -11.7565 10.8980 -1.079 0.280686
## 1994 - 1983 == 0 -11.2912 9.8365 -1.148 0.251013
## 1995 - 1983 == 0 -2.3895 9.8365 -0.243 0.808065
## 1997 - 1983 == 0 0.1474 8.8239 0.017 0.986676
## 1998 - 1983 == 0 -1.9930 10.9518 -0.182 0.855597
## 2000 - 1983 == 0 2.4801 9.8365 0.252 0.800939
## 2001 - 1983 == 0 3.2227 11.1584 0.289 0.772721
## 2002 - 1983 == 0 11.8698 9.8365 1.207 0.227544
## 2003 - 1983 == 0 14.2380 9.8365 1.447 0.147766
## 2004 - 1983 == 0 19.9820 10.8980 1.834 0.066721 .
## 2005 - 1983 == 0 17.8229 9.8365 1.812 0.069999 .
## 2006 - 1983 == 0 26.3586 11.1584 2.362 0.018165 *
## 2007 - 1983 == 0 21.1898 9.8365 2.154 0.031225 *
## 2010 - 1983 == 0 26.1775 9.8365 2.661 0.007785 **
## 2014 - 1983 == 0 29.1780 9.8365 2.966 0.003014 **
## 2015 - 1983 == 0 30.5888 9.8365 3.110 0.001873 **
## 2016 - 1983 == 0 22.5187 9.8365 2.289 0.022062 *
## 2017 - 1983 == 0 37.4821 9.8365 3.811 0.000139 ***
## 2018 - 1983 == 0 38.9633 9.8365 3.961 7.46e-05 ***
## 1985 - 1984 == 0 2.4413 6.1277 0.398 0.690334
## 1986 - 1984 == 0 7.8362 9.5407 0.821 0.411454
## 1987 - 1984 == 0 8.1562 9.5407 0.855 0.392619
## 1988 - 1984 == 0 9.0747 9.5407 0.951 0.341529
## 1989 - 1984 == 0 4.7278 8.1790 0.578 0.563237
## 1990 - 1984 == 0 5.8618 8.1790 0.717 0.473567
## 1992 - 1984 == 0 11.0912 9.5407 1.163 0.245030
## 1993 - 1984 == 0 11.9557 9.5407 1.253 0.210163
## 1994 - 1984 == 0 12.4209 8.3063 1.495 0.134820
## 1995 - 1984 == 0 21.3227 8.3063 2.567 0.010257 *
## 1997 - 1984 == 0 23.8595 7.1871 3.320 0.000901 ***
## 1998 - 1984 == 0 21.7191 9.8014 2.216 0.026697 *
## 2000 - 1984 == 0 26.1923 8.3063 3.153 0.001614 **
## 2001 - 1984 == 0 26.9349 9.6352 2.795 0.005183 **
## 2002 - 1984 == 0 35.5820 8.3063 4.284 1.84e-05 ***
## 2003 - 1984 == 0 37.9502 8.3063 4.569 4.90e-06 ***
## 2004 - 1984 == 0 43.6942 9.5407 4.580 4.66e-06 ***
## 2005 - 1984 == 0 41.5351 8.3063 5.000 5.72e-07 ***
## 2006 - 1984 == 0 50.0708 9.6352 5.197 2.03e-07 ***
## 2007 - 1984 == 0 44.9019 8.3063 5.406 6.45e-08 ***
## 2010 - 1984 == 0 49.8897 8.3063 6.006 1.90e-09 ***
## 2014 - 1984 == 0 52.8902 8.3063 6.367 1.92e-10 ***
## 2015 - 1984 == 0 54.3010 8.3063 6.537 6.26e-11 ***
## 2016 - 1984 == 0 46.2308 8.3063 5.566 2.61e-08 ***
## 2017 - 1984 == 0 61.1943 8.3063 7.367 1.74e-13 ***
## 2018 - 1984 == 0 62.6755 8.3063 7.546 4.51e-14 ***
## 1986 - 1985 == 0 5.3949 9.3775 0.575 0.565088
## 1987 - 1985 == 0 5.7149 9.3775 0.609 0.542243
## 1988 - 1985 == 0 6.6334 9.3775 0.707 0.479335
## 1989 - 1985 == 0 2.2865 8.0083 0.286 0.775246
## 1990 - 1985 == 0 3.4205 8.0083 0.427 0.669290
## 1992 - 1985 == 0 8.6499 9.3775 0.922 0.356315
## 1993 - 1985 == 0 9.5144 9.3775 1.015 0.310298
## 1994 - 1985 == 0 9.9797 8.1185 1.229 0.218976
## 1995 - 1985 == 0 18.8814 8.1185 2.326 0.020033 *
## 1997 - 1985 == 0 21.4182 6.9551 3.079 0.002074 **
## 1998 - 1985 == 0 19.2779 9.6175 2.004 0.045022 *
## 2000 - 1985 == 0 23.7510 8.1185 2.926 0.003438 **
## 2001 - 1985 == 0 24.4936 9.4995 2.578 0.009926 **
## 2002 - 1985 == 0 33.1407 8.1185 4.082 4.46e-05 ***
## 2003 - 1985 == 0 35.5089 8.1185 4.374 1.22e-05 ***
## 2004 - 1985 == 0 41.2529 9.3775 4.399 1.09e-05 ***
## 2005 - 1985 == 0 39.0938 8.1185 4.815 1.47e-06 ***
## 2006 - 1985 == 0 47.6295 9.4995 5.014 5.33e-07 ***
## 2007 - 1985 == 0 42.4607 8.1185 5.230 1.69e-07 ***
## 2010 - 1985 == 0 47.4484 8.1185 5.845 5.08e-09 ***
## 2014 - 1985 == 0 50.4489 8.1185 6.214 5.16e-10 ***
## 2015 - 1985 == 0 51.8597 8.1185 6.388 1.68e-10 ***
## 2016 - 1985 == 0 43.7896 8.1185 5.394 6.90e-08 ***
## 2017 - 1985 == 0 58.7530 8.1185 7.237 4.59e-13 ***
## 2018 - 1985 == 0 60.2342 8.1185 7.419 1.18e-13 ***
## 1987 - 1986 == 0 0.3200 11.8233 0.027 0.978408
## 1988 - 1986 == 0 1.2385 11.8233 0.105 0.916573
## 1989 - 1986 == 0 -3.1083 10.8048 -0.288 0.773591
## 1990 - 1986 == 0 -1.9743 10.8048 -0.183 0.855012
## 1992 - 1986 == 0 3.2550 11.8233 0.275 0.783083
## 1993 - 1986 == 0 4.1195 11.8233 0.348 0.727523
## 1994 - 1986 == 0 4.5848 10.8521 0.422 0.672676
## 1995 - 1986 == 0 13.4865 10.8521 1.243 0.213959
## 1997 - 1986 == 0 16.0234 9.9890 1.604 0.108690
## 1998 - 1986 == 0 13.8830 11.9675 1.160 0.246026
## 2000 - 1986 == 0 18.3561 10.8521 1.691 0.090746 .
## 2001 - 1986 == 0 19.0987 11.9683 1.596 0.110539
## 2002 - 1986 == 0 27.7458 10.8521 2.557 0.010566 *
## 2003 - 1986 == 0 30.1140 10.8521 2.775 0.005521 **
## 2004 - 1986 == 0 35.8580 11.8233 3.033 0.002423 **
## 2005 - 1986 == 0 33.6989 10.8521 3.105 0.001901 **
## 2006 - 1986 == 0 42.2347 11.9683 3.529 0.000417 ***
## 2007 - 1986 == 0 37.0658 10.8521 3.416 0.000637 ***
## 2010 - 1986 == 0 42.0535 10.8521 3.875 0.000107 ***
## 2014 - 1986 == 0 45.0540 10.8521 4.152 3.30e-05 ***
## 2015 - 1986 == 0 46.4648 10.8521 4.282 1.86e-05 ***
## 2016 - 1986 == 0 38.3947 10.8521 3.538 0.000403 ***
## 2017 - 1986 == 0 53.3581 10.8521 4.917 8.80e-07 ***
## 2018 - 1986 == 0 54.8393 10.8521 5.053 4.34e-07 ***
## 1988 - 1987 == 0 0.9185 11.8233 0.078 0.938078
## 1989 - 1987 == 0 -3.4283 10.8048 -0.317 0.751019
## 1990 - 1987 == 0 -2.2943 10.8048 -0.212 0.831839
## 1992 - 1987 == 0 2.9350 11.8233 0.248 0.803950
## 1993 - 1987 == 0 3.7995 11.8233 0.321 0.747940
## 1994 - 1987 == 0 4.2648 10.8521 0.393 0.694327
## 1995 - 1987 == 0 13.1665 10.8521 1.213 0.225028
## 1997 - 1987 == 0 15.7034 9.9890 1.572 0.115934
## 1998 - 1987 == 0 13.5630 11.9675 1.133 0.257082
## 2000 - 1987 == 0 18.0361 10.8521 1.662 0.096515 .
## 2001 - 1987 == 0 18.7787 11.9683 1.569 0.116639
## 2002 - 1987 == 0 27.4258 10.8521 2.527 0.011497 *
## 2003 - 1987 == 0 29.7940 10.8521 2.745 0.006043 **
## 2004 - 1987 == 0 35.5380 11.8233 3.006 0.002649 **
## 2005 - 1987 == 0 33.3789 10.8521 3.076 0.002099 **
## 2006 - 1987 == 0 41.9147 11.9683 3.502 0.000462 ***
## 2007 - 1987 == 0 36.7458 10.8521 3.386 0.000709 ***
## 2010 - 1987 == 0 41.7335 10.8521 3.846 0.000120 ***
## 2014 - 1987 == 0 44.7340 10.8521 4.122 3.75e-05 ***
## 2015 - 1987 == 0 46.1448 10.8521 4.252 2.12e-05 ***
## 2016 - 1987 == 0 38.0747 10.8521 3.509 0.000451 ***
## 2017 - 1987 == 0 53.0381 10.8521 4.887 1.02e-06 ***
## 2018 - 1987 == 0 54.5193 10.8521 5.024 5.06e-07 ***
## 1989 - 1988 == 0 -4.3468 10.8048 -0.402 0.687460
## 1990 - 1988 == 0 -3.2128 10.8048 -0.297 0.766198
## 1992 - 1988 == 0 2.0165 11.8233 0.171 0.864575
## 1993 - 1988 == 0 2.8810 11.8233 0.244 0.807485
## 1994 - 1988 == 0 3.3463 10.8521 0.308 0.757814
## 1995 - 1988 == 0 12.2480 10.8521 1.129 0.259055
## 1997 - 1988 == 0 14.7849 9.9890 1.480 0.138841
## 1998 - 1988 == 0 12.6445 11.9675 1.057 0.290709
## 2000 - 1988 == 0 17.1176 10.8521 1.577 0.114714
## 2001 - 1988 == 0 17.8602 11.9683 1.492 0.135622
## 2002 - 1988 == 0 26.5073 10.8521 2.443 0.014582 *
## 2003 - 1988 == 0 28.8755 10.8521 2.661 0.007795 **
## 2004 - 1988 == 0 34.6195 11.8233 2.928 0.003411 **
## 2005 - 1988 == 0 32.4604 10.8521 2.991 0.002779 **
## 2006 - 1988 == 0 40.9962 11.9683 3.425 0.000614 ***
## 2007 - 1988 == 0 35.8273 10.8521 3.301 0.000962 ***
## 2010 - 1988 == 0 40.8150 10.8521 3.761 0.000169 ***
## 2014 - 1988 == 0 43.8155 10.8521 4.038 5.40e-05 ***
## 2015 - 1988 == 0 45.2263 10.8521 4.168 3.08e-05 ***
## 2016 - 1988 == 0 37.1562 10.8521 3.424 0.000617 ***
## 2017 - 1988 == 0 52.1196 10.8521 4.803 1.57e-06 ***
## 2018 - 1988 == 0 53.6008 10.8521 4.939 7.84e-07 ***
## 1990 - 1989 == 0 1.1340 9.6537 0.117 0.906489
## 1992 - 1989 == 0 6.3633 10.8048 0.589 0.555905
## 1993 - 1989 == 0 7.2278 10.8048 0.669 0.503531
## 1994 - 1989 == 0 7.6931 9.7323 0.790 0.429254
## 1995 - 1989 == 0 16.5948 9.7323 1.705 0.088172 .
## 1997 - 1989 == 0 19.1317 8.7768 2.180 0.029272 *
## 1998 - 1989 == 0 16.9913 10.9967 1.545 0.122316
## 2000 - 1989 == 0 21.4644 9.7323 2.205 0.027421 *
## 2001 - 1989 == 0 22.2071 10.9284 2.032 0.042149 *
## 2002 - 1989 == 0 30.8541 9.7323 3.170 0.001523 **
## 2003 - 1989 == 0 33.2224 9.7323 3.414 0.000641 ***
## 2004 - 1989 == 0 38.9663 10.8048 3.606 0.000310 ***
## 2005 - 1989 == 0 36.8073 9.7323 3.782 0.000156 ***
## 2006 - 1989 == 0 45.3430 10.9284 4.149 3.34e-05 ***
## 2007 - 1989 == 0 40.1741 9.7323 4.128 3.66e-05 ***
## 2010 - 1989 == 0 45.1619 9.7323 4.640 3.48e-06 ***
## 2014 - 1989 == 0 48.1624 9.7323 4.949 7.47e-07 ***
## 2015 - 1989 == 0 49.5731 9.7323 5.094 3.51e-07 ***
## 2016 - 1989 == 0 41.5030 9.7323 4.264 2.00e-05 ***
## 2017 - 1989 == 0 56.4664 9.7323 5.802 6.56e-09 ***
## 2018 - 1989 == 0 57.9477 9.7323 5.954 2.61e-09 ***
## 1992 - 1990 == 0 5.2293 10.8048 0.484 0.628399
## 1993 - 1990 == 0 6.0938 10.8048 0.564 0.572760
## 1994 - 1990 == 0 6.5591 9.7323 0.674 0.500343
## 1995 - 1990 == 0 15.4608 9.7323 1.589 0.112150
## 1997 - 1990 == 0 17.9977 8.7768 2.051 0.040306 *
## 1998 - 1990 == 0 15.8573 10.9967 1.442 0.149301
## 2000 - 1990 == 0 20.3304 9.7323 2.089 0.036712 *
## 2001 - 1990 == 0 21.0731 10.9284 1.928 0.053820 .
## 2002 - 1990 == 0 29.7201 9.7323 3.054 0.002260 **
## 2003 - 1990 == 0 32.0884 9.7323 3.297 0.000977 ***
## 2004 - 1990 == 0 37.8323 10.8048 3.501 0.000463 ***
## 2005 - 1990 == 0 35.6733 9.7323 3.665 0.000247 ***
## 2006 - 1990 == 0 44.2090 10.9284 4.045 5.23e-05 ***
## 2007 - 1990 == 0 39.0401 9.7323 4.011 6.04e-05 ***
## 2010 - 1990 == 0 44.0279 9.7323 4.524 6.07e-06 ***
## 2014 - 1990 == 0 47.0284 9.7323 4.832 1.35e-06 ***
## 2015 - 1990 == 0 48.4391 9.7323 4.977 6.45e-07 ***
## 2016 - 1990 == 0 40.3690 9.7323 4.148 3.36e-05 ***
## 2017 - 1990 == 0 55.3324 9.7323 5.685 1.30e-08 ***
## 2018 - 1990 == 0 56.8137 9.7323 5.838 5.30e-09 ***
## 1993 - 1992 == 0 0.8645 11.8233 0.073 0.941712
## 1994 - 1992 == 0 1.3298 10.8521 0.123 0.902475
## 1995 - 1992 == 0 10.2315 10.8521 0.943 0.345777
## 1997 - 1992 == 0 12.7684 9.9890 1.278 0.201162
## 1998 - 1992 == 0 10.6280 11.9675 0.888 0.374504
## 2000 - 1992 == 0 15.1011 10.8521 1.392 0.164063
## 2001 - 1992 == 0 15.8437 11.9683 1.324 0.185567
## 2002 - 1992 == 0 24.4908 10.8521 2.257 0.024022 *
## 2003 - 1992 == 0 26.8590 10.8521 2.475 0.013323 *
## 2004 - 1992 == 0 32.6030 11.8233 2.758 0.005824 **
## 2005 - 1992 == 0 30.4439 10.8521 2.805 0.005026 **
## 2006 - 1992 == 0 38.9797 11.9683 3.257 0.001126 **
## 2007 - 1992 == 0 33.8108 10.8521 3.116 0.001836 **
## 2010 - 1992 == 0 38.7985 10.8521 3.575 0.000350 ***
## 2014 - 1992 == 0 41.7990 10.8521 3.852 0.000117 ***
## 2015 - 1992 == 0 43.2098 10.8521 3.982 6.84e-05 ***
## 2016 - 1992 == 0 35.1397 10.8521 3.238 0.001203 **
## 2017 - 1992 == 0 50.1031 10.8521 4.617 3.90e-06 ***
## 2018 - 1992 == 0 51.5843 10.8521 4.753 2.00e-06 ***
## 1994 - 1993 == 0 0.4653 10.8521 0.043 0.965802
## 1995 - 1993 == 0 9.3670 10.8521 0.863 0.388055
## 1997 - 1993 == 0 11.9039 9.9890 1.192 0.233378
## 1998 - 1993 == 0 9.7635 11.9675 0.816 0.414596
## 2000 - 1993 == 0 14.2366 10.8521 1.312 0.189562
## 2001 - 1993 == 0 14.9792 11.9683 1.252 0.210724
## 2002 - 1993 == 0 23.6263 10.8521 2.177 0.029472 *
## 2003 - 1993 == 0 25.9945 10.8521 2.395 0.016605 *
## 2004 - 1993 == 0 31.7385 11.8233 2.684 0.007266 **
## 2005 - 1993 == 0 29.5794 10.8521 2.726 0.006417 **
## 2006 - 1993 == 0 38.1152 11.9683 3.185 0.001449 **
## 2007 - 1993 == 0 32.9463 10.8521 3.036 0.002398 **
## 2010 - 1993 == 0 37.9340 10.8521 3.496 0.000473 ***
## 2014 - 1993 == 0 40.9345 10.8521 3.772 0.000162 ***
## 2015 - 1993 == 0 42.3453 10.8521 3.902 9.54e-05 ***
## 2016 - 1993 == 0 34.2752 10.8521 3.158 0.001586 **
## 2017 - 1993 == 0 49.2386 10.8521 4.537 5.70e-06 ***
## 2018 - 1993 == 0 50.7198 10.8521 4.674 2.96e-06 ***
## 1995 - 1994 == 0 8.9017 9.6537 0.922 0.356472
## 1997 - 1994 == 0 11.4386 8.6427 1.323 0.185670
## 1998 - 1994 == 0 9.2982 10.8340 0.858 0.390760
## 2000 - 1994 == 0 13.7713 9.6537 1.427 0.153713
## 2001 - 1994 == 0 14.5140 10.8343 1.340 0.180366
## 2002 - 1994 == 0 23.1610 9.6537 2.399 0.016431 *
## 2003 - 1994 == 0 25.5292 9.6537 2.645 0.008181 **
## 2004 - 1994 == 0 31.2732 10.8521 2.882 0.003955 **
## 2005 - 1994 == 0 29.1142 9.6537 3.016 0.002562 **
## 2006 - 1994 == 0 37.6499 10.8343 3.475 0.000511 ***
## 2007 - 1994 == 0 32.4810 9.6537 3.365 0.000766 ***
## 2010 - 1994 == 0 37.4688 9.6537 3.881 0.000104 ***
## 2014 - 1994 == 0 40.4693 9.6537 4.192 2.76e-05 ***
## 2015 - 1994 == 0 41.8800 9.6537 4.338 1.44e-05 ***
## 2016 - 1994 == 0 33.8099 9.6537 3.502 0.000461 ***
## 2017 - 1994 == 0 48.7733 9.6537 5.052 4.37e-07 ***
## 2018 - 1994 == 0 50.2545 9.6537 5.206 1.93e-07 ***
## 1997 - 1995 == 0 2.5369 8.6427 0.294 0.769119
## 1998 - 1995 == 0 0.3965 10.8340 0.037 0.970807
## 2000 - 1995 == 0 4.8696 9.6537 0.504 0.613959
## 2001 - 1995 == 0 5.6122 10.8343 0.518 0.604454
## 2002 - 1995 == 0 14.2593 9.6537 1.477 0.139653
## 2003 - 1995 == 0 16.6275 9.6537 1.722 0.084997 .
## 2004 - 1995 == 0 22.3715 10.8521 2.061 0.039256 *
## 2005 - 1995 == 0 20.2124 9.6537 2.094 0.036282 *
## 2006 - 1995 == 0 28.7482 10.8343 2.653 0.007968 **
## 2007 - 1995 == 0 23.5793 9.6537 2.443 0.014585 *
## 2010 - 1995 == 0 28.5670 9.6537 2.959 0.003085 **
## 2014 - 1995 == 0 31.5675 9.6537 3.270 0.001075 **
## 2015 - 1995 == 0 32.9783 9.6537 3.416 0.000635 ***
## 2016 - 1995 == 0 24.9082 9.6537 2.580 0.009875 **
## 2017 - 1995 == 0 39.8716 9.6537 4.130 3.62e-05 ***
## 2018 - 1995 == 0 41.3528 9.6537 4.284 1.84e-05 ***
## 1998 - 1997 == 0 -2.1404 9.9082 -0.216 0.828970
## 2000 - 1997 == 0 2.3327 8.6427 0.270 0.787230
## 2001 - 1997 == 0 3.0754 9.9541 0.309 0.757356
## 2002 - 1997 == 0 11.7224 8.6427 1.356 0.174991
## 2003 - 1997 == 0 14.0906 8.6427 1.630 0.103027
## 2004 - 1997 == 0 19.8346 9.9890 1.986 0.047072 *
## 2005 - 1997 == 0 17.6756 8.6427 2.045 0.040841 *
## 2006 - 1997 == 0 26.2113 9.9541 2.633 0.008458 **
## 2007 - 1997 == 0 21.0424 8.6427 2.435 0.014904 *
## 2010 - 1997 == 0 26.0302 8.6427 3.012 0.002597 **
## 2014 - 1997 == 0 29.0307 8.6427 3.359 0.000782 ***
## 2015 - 1997 == 0 30.4414 8.6427 3.522 0.000428 ***
## 2016 - 1997 == 0 22.3713 8.6427 2.588 0.009640 **
## 2017 - 1997 == 0 37.3347 8.6427 4.320 1.56e-05 ***
## 2018 - 1997 == 0 38.8160 8.6427 4.491 7.08e-06 ***
## 2000 - 1998 == 0 4.4731 10.8340 0.413 0.679697
## 2001 - 1998 == 0 5.2158 11.9191 0.438 0.661678
## 2002 - 1998 == 0 13.8628 10.8340 1.280 0.200699
## 2003 - 1998 == 0 16.2310 10.8340 1.498 0.134094
## 2004 - 1998 == 0 21.9750 11.9675 1.836 0.066325 .
## 2005 - 1998 == 0 19.8159 10.8340 1.829 0.067393 .
## 2006 - 1998 == 0 28.3517 11.9191 2.379 0.017375 *
## 2007 - 1998 == 0 23.1828 10.8340 2.140 0.032370 *
## 2010 - 1998 == 0 28.1705 10.8340 2.600 0.009317 **
## 2014 - 1998 == 0 31.1711 10.8340 2.877 0.004013 **
## 2015 - 1998 == 0 32.5818 10.8340 3.007 0.002635 **
## 2016 - 1998 == 0 24.5117 10.8340 2.262 0.023668 *
## 2017 - 1998 == 0 39.4751 10.8340 3.644 0.000269 ***
## 2018 - 1998 == 0 40.9563 10.8340 3.780 0.000157 ***
## 2001 - 2000 == 0 0.7426 10.8343 0.069 0.945352
## 2002 - 2000 == 0 9.3897 9.6537 0.973 0.330725
## 2003 - 2000 == 0 11.7579 9.6537 1.218 0.223234
## 2004 - 2000 == 0 17.5019 10.8521 1.613 0.106796
## 2005 - 2000 == 0 15.3428 9.6537 1.589 0.111987
## 2006 - 2000 == 0 23.8785 10.8343 2.204 0.027526 *
## 2007 - 2000 == 0 18.7097 9.6537 1.938 0.052612 .
## 2010 - 2000 == 0 23.6974 9.6537 2.455 0.014098 *
## 2014 - 2000 == 0 26.6979 9.6537 2.766 0.005682 **
## 2015 - 2000 == 0 28.1087 9.6537 2.912 0.003595 **
## 2016 - 2000 == 0 20.0386 9.6537 2.076 0.037917 *
## 2017 - 2000 == 0 35.0020 9.6537 3.626 0.000288 ***
## 2018 - 2000 == 0 36.4832 9.6537 3.779 0.000157 ***
## 2002 - 2001 == 0 8.6471 10.8343 0.798 0.424803
## 2003 - 2001 == 0 11.0153 10.8343 1.017 0.309296
## 2004 - 2001 == 0 16.7593 11.9683 1.400 0.161422
## 2005 - 2001 == 0 14.6002 10.8343 1.348 0.177792
## 2006 - 2001 == 0 23.1359 11.8233 1.957 0.050370 .
## 2007 - 2001 == 0 17.9670 10.8343 1.658 0.097248 .
## 2010 - 2001 == 0 22.9548 10.8343 2.119 0.034115 *
## 2014 - 2001 == 0 25.9553 10.8343 2.396 0.016591 *
## 2015 - 2001 == 0 27.3661 10.8343 2.526 0.011541 *
## 2016 - 2001 == 0 19.2959 10.8343 1.781 0.074912 .
## 2017 - 2001 == 0 34.2594 10.8343 3.162 0.001566 **
## 2018 - 2001 == 0 35.7406 10.8343 3.299 0.000971 ***
## 2003 - 2002 == 0 2.3682 9.6537 0.245 0.806211
## 2004 - 2002 == 0 8.1122 10.8521 0.748 0.454748
## 2005 - 2002 == 0 5.9531 9.6537 0.617 0.537453
## 2006 - 2002 == 0 14.4889 10.8343 1.337 0.181121
## 2007 - 2002 == 0 9.3200 9.6537 0.965 0.334328
## 2010 - 2002 == 0 14.3077 9.6537 1.482 0.138313
## 2014 - 2002 == 0 17.3082 9.6537 1.793 0.072986 .
## 2015 - 2002 == 0 18.7190 9.6537 1.939 0.052495 .
## 2016 - 2002 == 0 10.6489 9.6537 1.103 0.269987
## 2017 - 2002 == 0 25.6123 9.6537 2.653 0.007975 **
## 2018 - 2002 == 0 27.0935 9.6537 2.807 0.005008 **
## 2004 - 2003 == 0 5.7440 10.8521 0.529 0.596600
## 2005 - 2003 == 0 3.5849 9.6537 0.371 0.710375
## 2006 - 2003 == 0 12.1206 10.8343 1.119 0.263257
## 2007 - 2003 == 0 6.9518 9.6537 0.720 0.471454
## 2010 - 2003 == 0 11.9395 9.6537 1.237 0.216167
## 2014 - 2003 == 0 14.9400 9.6537 1.548 0.121718
## 2015 - 2003 == 0 16.3508 9.6537 1.694 0.090315 .
## 2016 - 2003 == 0 8.2807 9.6537 0.858 0.391017
## 2017 - 2003 == 0 23.2441 9.6537 2.408 0.016049 *
## 2018 - 2003 == 0 24.7253 9.6537 2.561 0.010430 *
## 2005 - 2004 == 0 -2.1591 10.8521 -0.199 0.842298
## 2006 - 2004 == 0 6.3767 11.9683 0.533 0.594175
## 2007 - 2004 == 0 1.2078 10.8521 0.111 0.911383
## 2010 - 2004 == 0 6.1955 10.8521 0.571 0.568064
## 2014 - 2004 == 0 9.1960 10.8521 0.847 0.396774
## 2015 - 2004 == 0 10.6068 10.8521 0.977 0.328373
## 2016 - 2004 == 0 2.5367 10.8521 0.234 0.815178
## 2017 - 2004 == 0 17.5001 10.8521 1.613 0.106832
## 2018 - 2004 == 0 18.9813 10.8521 1.749 0.080275 .
## 2006 - 2005 == 0 8.5357 10.8343 0.788 0.430789
## 2007 - 2005 == 0 3.3668 9.6537 0.349 0.727267
## 2010 - 2005 == 0 8.3546 9.6537 0.865 0.386801
## 2014 - 2005 == 0 11.3551 9.6537 1.176 0.239495
## 2015 - 2005 == 0 12.7659 9.6537 1.322 0.186040
## 2016 - 2005 == 0 4.6958 9.6537 0.486 0.626667
## 2017 - 2005 == 0 19.6592 9.6537 2.036 0.041706 *
## 2018 - 2005 == 0 21.1404 9.6537 2.190 0.028533 *
## 2007 - 2006 == 0 -5.1689 10.8343 -0.477 0.633302
## 2010 - 2006 == 0 -0.1811 10.8343 -0.017 0.986662
## 2014 - 2006 == 0 2.8194 10.8343 0.260 0.794688
## 2015 - 2006 == 0 4.2301 10.8343 0.390 0.696211
## 2016 - 2006 == 0 -3.8400 10.8343 -0.354 0.723020
## 2017 - 2006 == 0 11.1235 10.8343 1.027 0.304568
## 2018 - 2006 == 0 12.6047 10.8343 1.163 0.244667
## 2010 - 2007 == 0 4.9878 9.6537 0.517 0.605387
## 2014 - 2007 == 0 7.9883 9.6537 0.827 0.407962
## 2015 - 2007 == 0 9.3990 9.6537 0.974 0.330244
## 2016 - 2007 == 0 1.3289 9.6537 0.138 0.890510
## 2017 - 2007 == 0 16.2923 9.6537 1.688 0.091472 .
## 2018 - 2007 == 0 17.7735 9.6537 1.841 0.065604 .
## 2014 - 2010 == 0 3.0005 9.6537 0.311 0.755941
## 2015 - 2010 == 0 4.4113 9.6537 0.457 0.647705
## 2016 - 2010 == 0 -3.6588 9.6537 -0.379 0.704680
## 2017 - 2010 == 0 11.3046 9.6537 1.171 0.241594
## 2018 - 2010 == 0 12.7858 9.6537 1.324 0.185354
## 2015 - 2014 == 0 1.4108 9.6537 0.146 0.883813
## 2016 - 2014 == 0 -6.6594 9.6537 -0.690 0.490304
## 2017 - 2014 == 0 8.3041 9.6537 0.860 0.389680
## 2018 - 2014 == 0 9.7853 9.6537 1.014 0.310758
## 2016 - 2015 == 0 -8.0701 9.6537 -0.836 0.403176
## 2017 - 2015 == 0 6.8933 9.6537 0.714 0.475190
## 2018 - 2015 == 0 8.3745 9.6537 0.867 0.385671
## 2017 - 2016 == 0 14.9634 9.6537 1.550 0.121136
## 2018 - 2016 == 0 16.4446 9.6537 1.703 0.088482 .
## 2018 - 2017 == 0 1.4812 9.6537 0.153 0.878055
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)2. Stacked categories - Supplement? Uva Island
Only plots, not stats
Explore 4x5
Data4_5<-subset(cover, Location=="4x5")
Explore Uva chains
Data_Chain_Uva<-subset(cover, Location=="UvRf-Chains")By transect
Mean Chains
Uva_1m2
Data_Uva12<-subset(cover, Location=="Uva_1m2")By transect
Mean 1m2
Cover<-grid.arrange(Plot_45 , Plot_UvaChains, Plot_Uva1m2, ncol=1)
#ggsave(file="Outputs/Fig_S1.svg", plot=Cover, width=8, height=10)3. Supplementary datasets (Canal del Afuera and Secas)
Import data
# Read Canal de Afuera data (Pocillopora 2014-2018)
Data_CanalAfuera <- read.csv("CoverData/CA_cover.csv", header=TRUE, sep = ",")
#summary(Data_CanalAfuera)
# Read Secas data (Massives 1980-2018)
Data_Chain_SECAS <- read.csv("CoverData/Secas_cover.csv", header=TRUE, sep = ",")
#summary(Data_Chain_SECAS)
# Read Secas + Uva data (Massives 1980-2018)
Suplementary.masssives <- read.csv("CoverData/Massives_cover.csv", header=TRUE, sep = ",")
#summary(Suplementary.masssives)
# Format color
FILL <-c("#C77CFF", "#F8766D", "#00BA38", "#619CFF")Pocillopora non-Uva (Canal de Afuera)
Pocillopora_CA <- ggplot(Data_CanalAfuera, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(colour="#A3A500", alpha=0.3)+
stat_summary(fun.y=mean, geom="line", colour="#A3A500") +
stat_summary(fun.y=mean, geom="point", shape=21, size=2, alpha=0.8, fill="#A3A500") +
scale_y_continuous("Canal de afuera reef \n Pocillopora cover (%)",
limits = c(-2, 90), breaks = seq(0, 100, by=20),
expand = c(0,0.1))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
facet_grid(Location~., scales="free")+
ggtitle("a.")+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
facet_grid(Location~.)
Pocillopora_CA 
- LMER model
Data_CanalAfuera$Year_F<-as.factor(Data_CanalAfuera$YEAR)
model_CA <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Transect, data=Data_CanalAfuera)
summary(model_CA)## Linear mixed-effects model fit by REML
## Data: Data_CanalAfuera
## AIC BIC logLik
## 114.7784 118.3186 -52.38918
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 9.232427 4.216186
##
## Fixed effects: Pocillopora ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F2015 57.43305 4.143548 10 13.86084 0
## Year_F2016 57.00977 4.143548 10 13.75868 0
## Year_F2018 70.15725 4.143548 10 16.93169 0
## Correlation:
## Y_F2015 Y_F2016
## Year_F2016 0.827
## Year_F2018 0.827 0.827
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.05091857 -0.65554034 -0.05954312 0.42760030 1.72437930
##
## Number of Observations: 18
## Number of Groups: 6 anova(model_CA) plot(ranef(model_CA)) # Symmetrical scatter effects around zero?
plot(model_CA) # plot residuals vs fitted
resnorm1 <- resid(model_CA)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_CA))) # Coefficients of the model
plot(model_CA, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_CA, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_CA, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups #write.csv(year_groups, "Outputs/CanalPocilloTukey.csv", row.names = F)
# Effect plot
plot(emmeans(model_CA, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model CA predictions")
- Summary stats Pocillopora CA
Massives Secas
Massive_Secas <- ggplot(Data_Chain_SECAS, aes(x=YEAR, y=Massive)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
#geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
#geom_smooth(span = 0.2, se=T, colour="darkgray")+
stat_summary(fun.y=mean, geom="line") +
geom_point(aes(fill=Transect), alpha=0.5, shape=21) +
scale_y_continuous("Secas Island reef \n Non-Pocillopora scleractinians cover (%)",
limits = c(-2, 80), breaks = seq(0, 100, by=10),
expand = c(0,0.1)
)+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2)#,
#expand = c(0.1,0)
)+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
#facet_grid(Location~., scales="free_y")
ggtitle("b.")
Massive_Secas
- LMER model SECAS
Data_Chain_SECAS$Year_F<-as.factor(Data_Chain_SECAS$YEAR)
model_Secas <- lme(
Massive ~ -1 + Year_F, random = ~1|Transect, data=Data_Chain_SECAS)
summary(model_Secas)## Linear mixed-effects model fit by REML
## Data: Data_Chain_SECAS
## AIC BIC logLik
## 1734.272 1796.924 -849.1361
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 0.0004912232 7.641786
##
## Fixed effects: Massive ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F1975 1.891718 1.528357 231 1.237746 0.2171
## Year_F1976 0.898021 1.708755 231 0.525541 0.5997
## Year_F1977 1.621573 1.208273 231 1.342059 0.1809
## Year_F1978 1.679452 1.080712 231 1.554024 0.1215
## Year_F1980 18.183354 1.753146 231 10.371842 0.0000
## Year_F1983 0.385200 2.416545 231 0.159401 0.8735
## Year_F1997 0.225000 2.416545 231 0.093108 0.9259
## Year_F1998 0.904762 2.888324 231 0.313248 0.7544
## Year_F2000 0.000000 2.416545 231 0.000000 1.0000
## Year_F2002 0.158157 2.416545 231 0.065448 0.9479
## Year_F2003 0.500000 2.416545 231 0.206907 0.8363
## Year_F2004 0.300000 2.416545 231 0.124144 0.9013
## Year_F2005 0.200000 2.416545 231 0.082763 0.9341
## Year_F2010 1.200000 2.416545 231 0.496577 0.6200
## Year_F2015 0.264049 3.417511 231 0.077264 0.9385
## Year_F2018 0.070547 2.416545 231 0.029193 0.9767
## Correlation:
## Y_F1975 Y_F1976 Y_F1977 Y_F1978 Y_F1980 Y_F1983 Y_F1997 Y_F1998
## Year_F1976 0
## Year_F1977 0 0
## Year_F1978 0 0 0
## Year_F1980 0 0 0 0
## Year_F1983 0 0 0 0 0
## Year_F1997 0 0 0 0 0 0
## Year_F1998 0 0 0 0 0 0 0
## Year_F2000 0 0 0 0 0 0 0 0
## Year_F2002 0 0 0 0 0 0 0 0
## Year_F2003 0 0 0 0 0 0 0 0
## Year_F2004 0 0 0 0 0 0 0 0
## Year_F2005 0 0 0 0 0 0 0 0
## Year_F2010 0 0 0 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0 0
## Y_F2000 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2010 Y_F2015
## Year_F1976
## Year_F1977
## Year_F1978
## Year_F1980
## Year_F1983
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2002 0
## Year_F2003 0 0
## Year_F2004 0 0 0
## Year_F2005 0 0 0 0
## Year_F2010 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.379463717 -0.212198142 -0.075570702 -0.004047582 6.834475873
##
## Number of Observations: 256
## Number of Groups: 10 anova(model_Secas) plot(ranef(model_Secas)) # Symmetrical scatter effects around zero?
plot(model_Secas) # plot residuals vs fitted
resnorm1 <- resid(model_Secas)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_Secas))) # Coefficients of the model
plot(model_Secas, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_Secas, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_Secas, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups #write.csv(year_groups, "Outputs/SecasNonPocilloTukey.csv", row.names = F)
# Effect plot
plot(emmeans(model_Secas, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model Secas predictions")
- Summary stats Massives Secas
Figure S2: Massives Uva+Secas
Figure S1: Percentage of cover by other scleractinian coral (non-Pocillopora) in Uva Island (top panel) Secas Island (bottom panel) reefs. Uva Island Non-Pocillopora scleractinian cover was <3.2% of the benthos across datasets and years. Secas Island was the only site with a significant cover of massive species before 1982-83 ENSO 18.2% (± 25.5 sd). However, the cover was reduced to 0.4% (± 0.7) after the 1982-83 ENSO and has not recovered up to 2018 (massive’s cover <1.5% in all the surveys between 1983 and 2018).
Other Supplementary figures cover
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